Apparatus for and method of processing biological samples

ABSTRACT

The present invention provides systems, devices, apparatuses and methods for automated bioprocessing. Examples of protocols and bioprocessing procedures suitable for the present invention include but are not limited to: immunoprecipitation, chromatin immunoprecipitation, recombinant protein isolation, nucleic acid separation and isolation, protein labeling, separation and isolation, cell separation and isolation, food safety analysis and automatic bead based separation. In some embodiments, the invention provides automated systems, automated devices, automated cartridges and automated methods of western blot processing. Other embodiments include automated systems, automated devices, automated cartridges and automated methods for separation, preparation and purification of nucleic acids, such as DNA or RNA or fragments thereof, including plasmid DNA, genomic DNA, bacterial DNA, viral DNA and any other DNA, and for automated systems, automated devices, automated cartridges and automated methods for processing, separation and purification of proteins, peptides and the like.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.14/462,640 filed Aug. 19, 2014, which is a Continuation of U.S.application Ser. No. 13/615,500 filed Sep. 13, 2012 (now U.S. Pat. No.8,845,984), which is a Continuation of U.S. application Ser. No.12/549,311 filed Aug. 27, 2009 (now U.S. Pat. No. 8,404,198), whichclaims priority to U.S. Application No. 61/139,539 filed Dec. 19, 2008;U.S. Application No. 61/108,019 filed Oct. 23, 2008; U.S. ApplicationNo. 61/098,586 filed Sep. 19, 2008; and U.S. Application No. 61/092,338filed Aug. 27, 2008, which disclosures are herein incorporation byreference in their entirety.

FIELD OF THE INVENTION

The invention relates to apparatuses and methods for processingbiomolecules and more specifically to automated methods and apparatusesfor processing biomolecules.

BACKGROUND OF THE INVENTION

Certain laboratory procedures remain predominantly carried out usinginefficient manual methods which require individual attention by thescientist or lab technician performing the procedure. Many of theseprocedures would benefit from automation. For example, nucleic acidpurification, such as plasmid preparation is currently a time consuming,inefficient task that has not yet been automated. Gradual improvementssuch as the introduction of precipitation filters have reduced thehands-on time required, however even the most advanced nucleic acidpurification kits still require several hours and individual attention.Similarly, processing for western blot analysis can be a labor intensiveprocess that requires the scientist or lab technician to be tied to thebench during the process. In addition, such processes suffer from humanerror and lack of reproducibility inherent in manually intensiveprocedures. What is needed, and what is provided herein, in part, is asmall, affordable, user-friendly and flexible instrument for reactionsperformed on solid supports, preproteomics sample preparation, nucleicacid applications, and cell separation applications with increasedconvenience of use, reduced labor time, decreased error, and increasedreproducibility.

SUMMARY OF THE INVENTION

In some embodiments, the present invention provides systems, devices,apparatuses and methods for automated bioprocessing. Examples ofprotocols and bioprocessing procedures suitable for the presentinvention include but are not limited to: immunoprecipitation, chromatinimmunoprecipitation, recombinant protein isolation, nucleic acidseparation and isolation, protein labeling, separation and isolation,cell separation and isolation, and automatic bead based separation. In aparticular embodiment, the invention provides automated systems,automated devices, automated cartridges and automated methods of westernblot processing. Other embodiments include automated systems, automateddevices, automated cartridges and automated methods for separation,preparation and purification of nucleic acids, such as DNA or RNA orfragments thereof, including plasmid DNA, genomic DNA, bacterial DNA,viral DNA and any other DNA or fragments thereof, and for automatedsystems, automated devices, automated cartridges and automated methodsfor processing, separation and purification of proteins, peptides andthe like.

In some embodiments, an automated bioprocessing system includes abioprocessing device, at least one bioprocessing cartridge, a fluidsupply and a computer control system for controlling at least oneparameter associated with bioprocessing using the bioprocessingcartridge. In some embodiments, an automated bioprocessing system mayinclude multiple bioprocessing cartridges.

In some embodiments, automated bioprocessing devices include one or morecartridge slots, each slot configured to receive a bioprocessingcartridge; a removable fluid container tray comprising multiple fluidcontainer holders configured to hold fluid containers for use duringbioprocessing and a computer control system, configured to control atleast one parameter associated with bioprocessing in the one or morebioprocessing cartridges.

In some embodiments, automated bioprocessing devices include a fluidmanifold configured to fluidly connect one or more fluid containerswithin a fluid container holder with one or more process fluidconnectors. In some embodiments, the automated bioprocessing devices mayinclude a fluid manifold configured to connect one or more control fluidconnectors on a bioprocessing cartridge to one or more control fluidsupplies.

In some embodiments, the automated bioprocessing cartridges include atleast one bioprocessing chamber configured to contain a solid support,the cartridge further including a plurality of mesoscale and/ormicroscale fluid flow channels in fluid communication with thebioprocessing chamber through at least one pump.

In some embodiments, the automated methods of bioprocessing includeproviding a bioprocessing cartridge comprising at least onebioprocessing chamber containing a solid support and a plurality ofmesoscale and/or microscale fluid flow channels in fluid communicationwith the bioprocessing chamber, and pumping at least one processingfluid through at least one of the plurality of mesoscale or microscalefluid flow channels and into the bioprocessing chamber.

In some embodiments, provided herein is a bioprocessing cartridgecomprising at least one bioprocessing chamber configured to contain ablotting membrane, a plurality of mesoscale and/or microscale processfluid channels in fluid communication with the bioprocessing chamber,and a plurality of built-in pumps, configured for pumping fluid throughthe process fluid channels. The diameter of the process fluid channelsmay be in the range of between about 10 um and about 10 mm, betweenabout 100 um and about 5 mm, between about 250 um and about 2.5 mm,between about 500 um and about 2 mm, or about 1 mm in diameter. Thecartridge may be a plastic cartridge. The cartridge may further compriseno flexible tubing. In some embodiments, the cartridge may comprise atleast one access valve within a flow path defined by at least one of theplurality of process fluid channels. Each of the at least one accessvalves may be located within a flow bath between at least one processfluid connector and the at least one of the plurality of process fluidchannels, each process fluid connector configured to fluidly connect thecartridge to one or more fluid containers. In some embodiments, thecartridge may include more than one access valve, wherein each accessvalve may be placed within a flow path between and independent processfluid connector and one of the plurality of process fluid channels, eachindependent process fluid connector configured to fluidly connect thecartridge to one or more fluid containers. The process fluid connectorsmay be a plurality of connectors, such as for example, between 2 and 20aspiration and/or expiration tubes, between 2 and 10 aspiration and/orexpiration tubes, or between 4 and 8 aspiration and/or expiration tubes.In some embodiments, the cartridge may comprise an access valve withineach of the flow paths between each of the process fluid connectors andeach of the plurality of process fluid channels. In some embodiments,the cartridge may comprise an access valve within each of the flow pathsbetween each of the process fluid connectors and each of the pluralityof process fluid channels. In some embodiments, the cartridge mayinclude a blotting membrane within the bioprocessing chamber. Theblotting membrane may be a Western blotting membrane. The shape of thecartridge may vary. In some embodiments of the cartridge, the depth maybe in the range of between about 2 mm to about 5 cm, between about 4 mmto about 4 cm, between about 5 mm to about 2 cm, between about 8 mm toabout 1.5 cm, between about 9 mm to about 1.2 cm, about 1 cm, or 1 cm.The height of the cartridge may be in the range of between about 10 cmand about 25 cm, between about 12 cm and about 20 cm, between about 14cm and about 18 cm, between about 15 cm and about 17 cm, about 16 cm, or16 cm. The width of the cartridge at its greatest may be in the range ofbetween about 10 cm and about 25 cm, between about 12 cm and about 22cm, between about 16 cm and about 20 cm, between about 17 cm and about19 cm, about 18 cm, 18 cm, or about 18.2 cm, or 18.2 cm. In someembodiments, the cartridge may have a rectangular shape or a squareshape. The process fluid connectors may be in the range of between about10 um and about 10 mm in diameter, between about 100 um and about 5 mmin diameter, between about 250 um and about 2.5 mm in diameter, betweenabout 500 um and about 2.0 mm in diameter, or about 1 mm in diameter.The cartridge in some embodiments, may be enclosed by a package. In someembodiments, the at least one process fluid connector may have adiameter that tapers to a smaller inner diameter at its distal end. Insome embodiments, the inside diameter of the at least one process fluidconnector closest (proximal) to the process fluid channel, is about 0.5mm to about 15 mm, about 1 mm to about 10 mm, about 2 mm to about 6 mm,about 4 mm, or 4 mm, and the inside diameter of the end of the at leastone process fluid connectors furthest (distal) from the process fluidchannel, has an inner diameter of between about 10 μm and about 10 mm,between about 100 μm and about 5 mm, between about 250 μm and about 2.5mm, between about 500 μm and about 2.0 mm in diameter, or about 1 mm indiameter. The cartridge may comprise any combination of elements asprovided in the specification.

Provided herein, in some embodiments, is an automated blot processingdevice comprising: one or more cartridge slots, each slot configured toreceive a bioprocessing cartridge, and an automated control system,configured to control at least one step associated with processing ablotting membrane within the bioprocessing cartridge in a blottingprotocol. In some embodiments, the device may comprise between about 1to about 8, between about 2 to about 6, between about 3 to about 5, or 4cartridge slots. In some embodiments, the device may further comprise abioprocessing cartridge. The bioprocessing cartridge may include a blot,wherein the blot is a western blot, and the blotting protocol is awestern blot processing protocol. In some embodiments the blotprocessing device may further comprise a blotting membrane within thebioprocessing cartridge. The automated control system may be configuredto automatically control most steps, all steps or all steps except one,two, three, or four steps of a blot processing protocol, such as awestern blot processing protocol. In some embodiments, the automatedblot processing device may include an automated control systemconfigured to eliminate the need for all, all but 1, all but 2, or allbut 3 steps of a blot processing protocol, such as a western blotprocessing protocol. The automated blot processing device may be anydevice according to any of the embodiments of the device providedherein. The automated blot processing device may use any bioprocessingcartridge described herein in the specification.

In some embodiments, an automated method of bioprocessing includes: a)inserting at least one bioprocessing cartridge into an automatedbioprocessing device, said bioprocessing cartridge comprising: i) atleast one bioprocessing chamber containing a solid support therein; andii) a plurality of mesoscale and/or microscale channels in fluidconnection with to said bioprocessing chamber; and b) initiating abioprocessing protocol on said bioprocessing device, said protocolcomprising one or more of the following: i) controlling pumps and valveson said bioprocessing cartridge to supply reagents and/or samples fromone or more containers to the at least one bioprocessing chamber of eachof the at least one bioprocessing cartridges, ii) controlling pumps andvalves on said bioprocessing cartridge to recirculate the reagents andor samples across the at least one bioprocessing chamber of each of theat least one bioprocessing cartridges; and/or iii) controlling pumps andvalves on said bioprocessing cartridge to remove reagents and/or samplesfrom the at least one bioprocessing chamber of each of the at least onebioprocessing cartridges.

In some embodiments, the methods include methods of applying one or morefluids to a solid support comprising: a) inserting at least onebioprocessing cartridge into an automated bioprocessing device, saidbioprocessing cartridge comprising: i) at least one bioprocessingchamber containing a solid support therein; and ii) a plurality ofmesoscale and/or microscale channels in fluid communication with the atleast one bioprocessing chamber; b) performing a pumping sequence on thecartridge, wherein the pumping sequence includes one or more fluidaddition cycles wherein fluid is pumped from one or more containersthrough at least one of the plurality of mesoscale and/or microscalechannels and into the at least one chamber.

Provided herein are automated methods of processing a blot comprising a)providing a bioprocessing cartridge according to any embodiment of thebioprocessing cartridge described herein, wherein the bioprocessingcartridge contains a blotting membrane; and pumping at least one processfluid through at least one of said plurality of process fluid channelsand into said bioprocessing chamber. In some embodiments, the method maybe performed by a device according to any of the bioprocessing devicesdescribed herein. The method may comprise all the steps, all but onestep, all but two steps, or all but three of the steps of a blottingprotocol performed on the blotting membrane by the device.

In some embodiments, the automated bioprocessing systems, automatedbioprocessing devices, automated bioprocessing cartridges, and automatedbioprocessing methods comprise western blot processing systems, westernblot processing devices, western blot processing cartridges, and westernblot processing methods.

In some embodiments, the automated bioprocessing systems, automatedbioprocessing devices, automated bioprocessing cartridges, and automatedbioprocessing methods comprise nucleic acid separation, purificationand/or collection systems, nucleic acid separation, purification and/orcollection devices, nucleic acid separation, purification and/orcollection cartridges, and nucleic acid separation, purification and/orcollection methods.

Further provided herein is a kit comprising any of the bioprocessingcartridges described herein in. The kit may further include one or moretubes, containers, or any other suitable fluid reservoirs.

Provided herein is a bioprocessing cartridge comprising at least onebioprocessing chamber configured to contain a solid support and aplurality of mesoscale and/or microscale process fluid channels in fluidcommunication with the bioprocessing chamber through at least one pump,wherein the at least one pump is included in or on the bioprocessingcartridge. In some embodiments, the cartridge may include at least oneaccess valve within a flow path defined by at least one of the pluralityof process fluid channels. Each of said at least one access valves maybe located within a flow path between a process fluid connector and theat least one of the plurality of process fluid channels, each processfluid connector configured to fluidly connect the cartridge to one ormore fluid containers. In some embodiments, the cartridge may includemore than one access valve, wherein each access valve is placed within aflow path between an independent process fluid connector and one of theplurality of process fluid channels, each independent process fluidconnector configured to fluidly connect the cartridge to one or morefluid containers. In some embodiments, the process fluid connectors maybe configured to connect to said fluid containers via a manifold. Insome embodiments, the process fluid connectors are configured to connectto said fluid containers via aspiration and/or expiration tubes. In someembodiments, the process fluid connectors may be aspiration and/orexpiration tubes. In some embodiments, the cartridge may include anaccess valve within each of the flow paths between each of the processfluid connectors and each of the plurality of process fluid channels.The solid support may be selected from the group consisting of: blottingmembranes, filter cassettes, filter membranes, filter papers, solidphase extraction cassettes, solid phase extraction disks, pluralities ofbeads, including magnetic beads, and combinations thereof. In someembodiments, the bioprocessing cartridge may include at least one, atleast two, or at least three process valves in a flow path between thepump and the chamber. In some embodiments, the at least one of saidprocess valves or said access valves includes an actuator to close thevalve and/or to open the valve. In some embodiments, at least one of theprocess valves and/or said access valves may include a check valve. Insome embodiments, the bioprocessing cartridge may include two or more,or three or more bioprocessing chambers. In some embodiments, thecartridge may further include a plurality of control fluid channels. Insome embodiments, the cartridge may further include control fluidconnectors connecting to each of said plurality of control fluidchannels, each control fluid connector configured to fluidly connect thecartridge to one or more automated control systems. In some embodiments,the automated control system controls the opening and closing of theprocess valves and the access valves and controls the at least one pump.In some embodiments, the cartridge may include a dye chamber in fluidcommunication with at least one process fluid channel, wherein amaterial within said dye chamber changes color when contacted with afluid. In some embodiments, the cartridge may include a multi-usecartridge. The processing chambers may, in some embodiments, beconfigured to provide access to the processing chambers by a user. Insome embodiments, the cartridge is a single use cartridge.

Further provided herein is an automated bioprocessing device comprisingone or more cartridge slots, each slot configured to receive abioprocessing cartridge, a removable fluid container tray comprising atleast one fluid container holder configured to hold containers for useduring bioprocessing, and an automated control system, configured tocontrol at least one parameter associated with bioprocessing in one ormore bioprocessing cartridges. The device may include 2 to 8 cartridgeslots or 2 to 4 cartridge slots. In some embodiments, the cartridgeslots may further include a fluid manifold configured to fluidly connectone or more fluid containers within the fluid container holder with oneor more process fluid connectors and/or a control fluid manifoldconfigured to connect one or more control fluid connectors to one ormore automated control systems. The manifold may be configured toconnect one or more control fluid connectors to one or more automatedcontrol systems. In some embodiments, the one or more automated controlsystems includes a vacuum supply and an air pressure supply. The vacuumsupply and/or said air pressure supply may be included within thedevice. Alternatively, the vacuum supply and/or said air pressure supplymay be external to the device. In some embodiments the vacuum supply mayinclude a vacuum pump. In some embodiments, the air pressure supply mayinclude a compressor. In some embodiments, the cartridge slots mayinclude multiple openings or guide features for receiving aspirationand/or expiration tubes on a cartridge and guiding the aspiration and/orexpiration tubes into fluid containers in the fluid container holders.In some embodiments of the device, the device may include at least oneremovable fluid container tray includes a set of fluid container holdersor reservoirs configured to supply reagents and/or samples to eachbioprocessing cartridge in each cartridge slot. The set of fluidcontainer holders further comprises containers configured to receivefluids from or supply fluids to each of multiple bioprocessingcartridges. In some embodiments, the bioprocessing device may include aGUI. In some embodiments, the automated control system may independentlyprovide for control of the pumps and the valves on bioprocessingcartridges in each of the cartridge slots. In some embodiments, theautomated control system may provide for user input of one or morecontrol parameters, user selection of pre-programmed protocols and/oruser creation and storage of protocols.

Further provided herein a method of using an automated method ofbioprocessing comprising: providing a bioprocessing cartridge comprisingat least one bioprocessing chamber containing a solid support therein,and a plurality of mesoscale and/or microscale process fluid channels influid communication with said bioprocessing chamber, and pumping atleast one process fluid through at least one of said plurality ofprocess fluid channels and into said bioprocessing chamber. In someembodiments, the pumping may include pumping one or more reagents and/ora sample into said processing chamber and into contact with the solidsupport. Additionally, the pumping may include circulating at least oneof said reagents from a channel accessing an upper portion of saidchamber through a pump on said cartridge and into a channel accessing abottom portion of said chamber. In some embodiments of the method, thepumping includes pumping at least one process fluid through or acrossthe surface of a filter or membrane in said at least one bioprocessingchamber. In some embodiments, the filter or membrane may include a blotmembrane. In some embodiments, the blot membrane may be held by a blotmembrane holder within the bioprocessing chamber. In some embodiments,the filter or membrane may include a western blot membrane. In someembodiments, the filter or membrane may include a cell separationmembrane. In some embodiments, the filter or membrane may include alysate filter. In some embodiments, the at least one process fluid mayinclude at least one blocking buffer. The at least one process fluid mayinclude at least one antibody and/or at least one washing fluid. In someembodiments of the method, the pumping may include: a) adding a blockingbuffer to the bioprocessing chamber, b) recirculating the blockingbuffer across a blot membrane to form a blocked blot membrane, c) addingat least one antibody solution to the bioprocessing chamber, and d)recirculating the at least one antibody solution across said blockedblot membrane. The recirculating at least one antibody solution acrosssaid blocked blot membrane may include: a) recirculating a primaryantibody solution across said blocked blot membrane, b) washing the blotmembrane, c) adding a secondary antibody solution to the bioprocessingchamber; and d) recirculating the secondary antibody solution across thewashed blot membrane. In some embodiments of the method the pumping mayinclude pumping at least one process fluid through at least one solidphase extraction membrane, at least one solid phase extraction cassetteor at least one solid phase extraction disk in at least onebioprocessing chamber. In some embodiments of the method, the solidphase extraction membrane, solid phase extraction cassette or solidphase extraction disk may include a silica reversible binding ligand. Insome embodiments, the pumping may include pumping cell culture mediaacross a cell separation filter to separate cells from the cell culturemedia, wherein said cells are captured on the filter. In someembodiments, the pumping may further include: a) resuspending thecaptured cells in a resuspension buffer, b) lysing the cell in a lysingsolution to form a lysate, c) neutralizing the lysate; and d) clarifyingthe lysate. The cells may be resuspended and pumped out of thebioprocessing chamber and into a container containing a lysing solution.In some embodiments, the clarifying the lysate may include pumping thelysate through a filter or membrane to remove unwanted cellularmolecules. In some embodiments of the method, the pumping may furtherinclude: a) extracting at least one biomolecule in a bioprocessingchamber containing a binding membrane, b) washing the binding membrane;and c) eluting the biomolecule from the binding membrane. In someembodiments of the method, the pumping may further include precipitatingthe biomolecule in a bioprocessing chamber containing a precipitationfilter. In some embodiments of the method, the method may furtherinclude pretreating the sample prior to the pumping. In someembodiments, the pretreating may include adding a salt solution to asample. In some embodiments, the salt solution may be NaCl.

Further provided herein is an automated method of bioprocessingcomprising: a) inserting at least one bioprocessing cartridge into abioprocessing device, said bioprocessing cartridge comprising: i) atleast one bioprocessing chamber containing a solid support therein, andii) a plurality of mesoscale and/or microscale channels in fluidcommunication with said bioprocessing chamber, b) initiating abioprocessing protocol on said bioprocessing device, said protocolcomprising one or more of the following: i) controlling pumps and valveson said bioprocessing cartridge to supply reagents and/or samples fromone or more containers to the at least one bioprocessing chamber of eachof the at least one bioprocessing cartridges, ii) controlling pumps andvalves on said bioprocessing cartridge to recirculate the reagents andor samples across the at least one bioprocessing chamber of each of theat least one bioprocessing cartridges; and/or iii) controlling pumps andvalves on said bioprocessing cartridge to remove reagents and/or samplesfrom the at least one bioprocessing chamber of each of the at least onebioprocessing cartridges.

Provided herein is a method of applying one or more fluids to a solidsupport comprising: a) inserting at least one bioprocessing cartridgeinto a bioprocessing device, said bioprocessing cartridge including: i)at least one bioprocessing chamber containing a solid support therein;and ii) a plurality of mesoscale and/or microscale channels in fluidcommunication with said bioprocessing chamber; b) performing a pumpingsequence on said cartridge, wherein said pumping sequence comprisesentering one or more fluid addition cycles wherein fluid is pumped fromthe one or more containers through one of the fluid flow channels andinto the chamber; wherein the fluid added in any of the fluid additioncycles is the same or different than fluid added in any other of thefluid addition cycles. In some embodiments, the pumping sequence mayfurther include entering a purging cycle following each fluid additioncycle comprising pumping fluid within the chamber into a designatedwaste container. In some embodiments of the method, the pumping sequencefurther comprises entering a circulating cycle after any of the fluidaddition cycles, wherein said circulating cycle comprises opening avalve in a fluid flow channel connected to the bottom of the chamber andpumping fluid from the bottom portion of the chamber through one or morefluid flow channels and into a top portion of the chamber. In someembodiments of the method, the method may further include initiating andterminating the pumping sequence using a programmable controller. Insome embodiments, the method may further include independently openingand closing valves in each of the process fluid connectors toselectively control the amount of fluid entering or leaving the fluidflow channels. In some embodiments, the method may further includeinserting multiple cartridges into the cartridge slots and performing apumping sequence on each of the cartridges, wherein the pumping sequenceperformed on each cartridge is the same or different than the pumpingsequence performed on any other cartridge. The pumping sequencesperformed on each of the cartridges may be performed at the same time.In some embodiments, the method may further include initiating andterminating the pumping sequence on each of the cartridges using aprogrammable controller. In some embodiments, the controller may be acentral processing unit of a computer. In some embodiments, the methodmay further include storing one or more selectable programs on saidcontroller. In some embodiments, the method may further includeinitiating a designated pumping sequence by selecting a program storedon said controller. In some embodiments, the method may further includedisplaying the one or more selectable programs on a GUI.

Further provided herein is an automated bioprocessing system comprising:a) a bioprocessing device comprising: i) one or more cartridge slots,each slot configured to receive a bioprocessing cartridge, and ii) anautomated control system, configured to control at least one parameterassociated with bioprocessing in one or more bioprocessing cartridges,and b) one or more bioprocessing cartridges comprising i) at least onebioprocessing chamber configured to contain a solid support, ii) aplurality of mesoscale and/or microscale process fluid channels in fluidcommunication with the bioprocessing chamber through at least one pump,wherein the at least one pump is included in or on the bioprocessingcartridge.

As used herein, card, cartridge, bioprocessing card and bioprocessingcartridge are intended to be interchangeable. Further provided herein isa cartridge, device, or method of any of the prior embodiments describedherein, wherein the blot comprises proteins or nucleic acids.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIGS. 1A-1D depict alternate embodiments of a bioprocessing device;

FIGS. 2A-2C depict alternate rear views of a bioprocessing device;

FIGS. 3A & 3B show embodiments of a graphical user interface (GUI);

FIG. 4 shows an exploded view of an embodiment of a bioprocessingdevice;

FIG. 5 shows an embodiment of a bioprocessing device with externalhousing removed;

FIG. 6 shows an exploded view of an embodiment of a removable fluidcontainer tray;

FIG. 7 shows an exploded view of an embodiment of a fluid containerholder;

FIGS. 8A-8G show various views and embodiments of a reagent tray andreagent reservoirs;

FIGS. 9A & 9B show perspective views of an embodiment of a cartridgeholder;

FIGS. 10A and 10B show side views of an embodiment of a cartridgeholder;

FIGS. 11A and 11B show cross-sectional views of an embodiment of acartridge holder;

FIG. 12 shows an exploded view of an embodiment of a bioprocessingcartridge;

FIGS. 13A & 13B show front and rear views of an embodiment of abioprocessing cartridge, respectively;

FIG. 14 shows a transparent view of an embodiment of a bioprocessingcartridge showing front and rear layers;

FIG. 15 shows a detail view of an embodiment of the connection between aprocess fluid connector and an aspiration/expiration tube;

FIG. 16A an exploded view of an embodiment of a bioprocessing cartridge;FIGS. 16B-16D show close-up views of portions of the bioprocessingcartridge shown in FIG. 16A;

FIGS. 17A & 17B show front and rear layer views of an embodiment of abioprocessing cartridge;

FIGS. 18A & 18B show front and rear views of an embodiment of abioprocessing cartridge;

FIGS. 19A & 19B show a interior and exterior views, respectively, of anembodiment of a bioprocessing cartridge;

FIGS. 20A & 20B show an alternate embodiment of a bioprocessingcartridge;

FIGS. 21A and 21B show detail views of blot membrane holders that may beinserted into embodiments of the bioprocessing cartridges;

FIGS. 22A and 22B show alternative embodiments of blot membrane holders;

FIG. 23 shows a high level flow chart of the basic user interface foroperation of an embodiment of a bioprocessing device;

FIGS. 24A & 24B shows results of a the western blots performed asdescribed in Examples 1 and 2;

FIGS. 25A & 25B shows the results of the western blots performed asdescribed in Examples 3 and 4;

FIGS. 26A-26E shows the results of the western blots performed asdescribed in Examples 5, 6, 7, 8 and 9;

FIGS. 27A-27D shows the results of the western blots performed asdescribed in Examples 10A and 10B and Examples 11A and 11B;

FIGS. 28A & 28B shows the results of the western blots performed asdescribed in Examples 12A and 12B;

FIGS. 29A & 29B shows the results of the western blots performed asdescribed in Examples 13A and 13B;

FIGS. 30A & 30B shows the results of the western blots performed asdescribed in Examples 14A and 14B;

FIGS. 31A-31D shows the results of the western blots performed asdescribed in Examples 16A and 16B and Examples 15A and 15B;

FIGS. 32A-32D shows the results of the western blots performed asdescribed in Examples 18A and 18B and Examples 17A and 17B

FIGS. 33A & 33B shows the results of the western blots performed asdescribed in Examples 19A and 19B;

FIGS. 34A & 34B shows the results of the western blots performed asdescribed in Examples 20A and 20B;

FIGS. 35A & 35B shows the results of the western blots performed asdescribed in Examples 21A and 21B;

FIGS. 36A & 36B shows the results of the western blots performed asdescribed in Examples 22A and 22B;

FIG. 37 shows the results of the nucleic acid purification performed asdescribed in Example 23;

FIG. 38 shows the results of the nucleic acid purification performed asdescribed in Example 24;

FIG. 39 shows the results of the nucleic acid purification performed asdescribed in Example 25;

FIG. 40 shows the results of the nucleic acid purification performed asdescribed in Example 26;

FIGS. 41A-41F show the results of the western blots performed asdescribed in Example 27;

FIGS. 42A-42C show the result of the western blots performed asdescribed in Example 27;

FIGS. 43A-43F show the result of the western blots performed asdescribed in Example 27;

FIGS. 44A & 44B show the results of the nucleic acid purificationperformed as described in Example 30;

FIGS. 45A & 45B show the results of the nucleic acid purificationperformed as described in Example 31; and

FIG. 46 shows the results of the nucleic acid purification performed asdescribed in Example 32.

DETAILED DESCRIPTION

The automated bioprocessing systems, automated bioprocessing devices,automated bioprocessing cartridges and automated bioprocessing methodsdisclosed herein include automated bioprocessing systems, automatedbioprocessing devices, automated bioprocessing cartridges and automatedbioprocessing methods for performing one or more protocols forprocessing biomolecules, such as for performing bioprocessing proceduresselected from: immunoprecipitation, chromatin immunoprecipitation,recombinant protein isolation, nucleic acid separation and isolation,protein labeling, separation and isolation, cell separation andisolation, food safety analysis, and automatic bead based separation,including automatic magnetic bead based separations. In someembodiments, the bioprocessing system may include the use of labeledmolecules, wherein the labels include, for example, immunofluorescenceor fluorescent labels, including Qdot® nanocrystals or Alexa Fluor®dyes. In some embodiments, the protocols for processing biomolecules areprotocols for processing biomolecules that are immobilized on a solidsupport, such as a blotting membrane with bound biomolecules. As such,the protocols can be protocols for processing Western blots (i.e.,immunoblots), Northern blots, or Southern blots. The automatedbioprocessing systems, automated bioprocessing devices, automatedbioprocessing cartridges and automated bioprocessing methods disclosedherein provide for automated “hands-off” bioprocessing once a protocolis initiated on a bioprocessing device, while delivering performancethat: is at least as good, if not better than similar manual processing;minimizes contamination/cleanup; and/or increases efficiency andflexibility.

I. BIOPROCESSING DEVICES

In some embodiments, the automated bioprocessing devices provided hereincomprise automated devices for performing one or more protocols forprocessing biomolecules. In some embodiments, the bioprocessing devicesmay be configured to run protocols and bioprocessing procedures selectedfrom: immunoprecipitation, chromatin immunoprecipitation, recombinantprotein isolation, nucleic acid separation and isolation, proteinlabeling, separation and isolation, cell separation and isolation, foodsafety and automatic bead based separation, including automatic magneticbead based separation.

In some embodiments, the automated bioprocessing devices include one ormore slots, such as two or more, three or more, four or more, five ormore, or six or more slots for receiving bioprocessing cartridges. Eachslot may independently be configured to receive and/or support abioprocessing cartridge within the device and to provide for fluidconnection of the cartridge to one or more fluid containers that may beused with the device. Each slot may further include a cartridge holder.In some embodiments, the slots each include a fluid manifold forconnecting the bioprocessing cartridges to one or more process fluidsupplies. In some embodiments, the slots include openings for receivinga cartridge and may guide one or more aspiration/expiration tubes intoone or more process fluid containers, such as one or more process fluidcontainers placed in or included within the device. In some embodiments,each of the slots comprise a single opening that includes at least oneguide, such as a projection or groove on one or both sides of the slotand/or cartridge holder that guide one or more aspiration/expirationtubes into one or more process fluid containers, such as one or moreprocess fluid containers placed in or included within the device. Insome embodiments, the aspiration/expiration tubes are integral to thebioprocessing cartridges or may be attached to fluid connectors on thebioprocessing cartridges. Each aspiration/expiration tube may be sizedappropriately to serve the function with which it is identifiedaccording to bioprocessing protocols included on the central processingunit on the device or according to user selected protocols. Theaspiration/expiration tubes may be the same length or may vary inlength, with respect to each other.

In some embodiments, each of the slots provides for connection of one ormore control fluid supplies to bioprocessing cartridges placed withinthe slots. Such connections, may, for example, include connection of acontrol fluid manifold to a cartridge inserted in each slot. In someembodiments, the control fluid manifold is configured to form a sealedconnection with control fluid connectors on a bioprocessing cartridgewithin the slot. In some embodiments, the control fluid manifold isconnected or sealed to the bioprocessing cartridge, in part, by using agasket or O-ring, or other suitable sealing mechanism. The control fluidmanifold may include individual supply connectors for interacting witheach of the control fluid connectors on a bioprocessing cartridge. Insome embodiments, the control fluid manifolds are reconfigurable,removable and/or replaceable to provide for alternative configurationsof the control fluid connectors on the bioprocessing cartridges. In someembodiments, the control fluid manifold may be urged onto or connectedto the control fluid connectors on a bioprocessing cartridge using apressurizable, inflatable, flexible container, such as a sack or abladder which, upon inflation, causes the supply connectors to movetowards and to be connected, such as sealably connected, to the controlfluid connectors on the bioprocessing cartridge. In some embodiments,mechanical mechanisms such as spring loaded mechanisms or automatic ormanual locking mechanisms may be used to connect the control fluidmanifold to the control fluid connectors.

In some embodiments, the control fluid manifold is used to supply acontrol fluid, such as air pressure, vacuum, or a pressurized liquid tovarious control channels on a bioprocessing cartridge via the controlfluid connectors in conjunction with the individual supply connectors.In some embodiments, the control fluid is used to provide pressureand/or vacuum on a non-contact side of a pump or valve membrane (i.e. aside of the membrane that does not come into contact with the processfluids) on a bioprocessing cartridge to actuate the pump or valve. Thisactuation may serve to open or close the valves and/or to cause thepumps to pump fluids through the process fluid channels on abioprocessing cartridge. By using specific defined protocols included inan automated control system, the pumps and valves may be controlled bysupplying pressure and/or vacuum to the pumps and valves to control theactuation of the various valves or pumps in specific orders or accordingto specific instructions to perform one or more bioprocesses on abioprocessing cartridge.

Though throughout the remainder of this application, the control fluidssupplied may be specifically referred to as air pressure and vacuum, itshould be understood that other control fluids may be used to performthe individual control steps, including both other gaseous controlfluids, such as nitrogen or oxygen or enriched air and the like, andother liquid control fluids. In addition, in some embodiments, one ormore of the control fluids may be treated prior to entering thebioprocessing cartridge and/or the control fluid manifold. Suchtreatment may include, purification, such as via filtration, enrichment,pressure regulation, de-humidification, humidification and the like toassist with efficient processing.

Each of the individual supply connectors may be in fluid communicationwith a pressure source and/or a vacuum source. The pressure sourceand/or vacuum source may comprise an external pressure or vacuum sourcesuch as a “house” air pressure supply and/or a “house” vacuum supply. Insome embodiments, the device includes a vacuum pump and/or a compressorand one or both of the vacuum and the air pressure may be supplied tothe bioprocessing cartridges without use of external supplies. Thedevice may also include appropriate pressure gauges and regulators tohelp control the amount of pressure supplied to each of the supplyconnectors and thus to the control channels and the valves and pumps andin some embodiments, the device includes reservoirs for storing pressureand vacuum to be supplied to the cartridge and to limit or avoidpressure or vacuum shortages or delays caused by delay in the supply ofpressure or vacuum, such as a delay caused by the response time of thecompressor and/or vacuum pump.

Alternatively, instead of a control fluid manifold, in some embodiments,some or all of the control fluid connectors on a bioprocessing cartridgemay be connected individually to a vacuum and pressure source.

In some embodiments, the slots on the bioprocessing device may bereconfigurable, removable and/or replaceable to provide for differentconfigurations, sizes or types of bioprocessing cartridges. The slotsmay include various guides, holes, holders, or any combination thereof,to ensure that the bioprocessing cartridges may be retained in the slotsat a correct height and orientation to perform the desired bioprocess.In some embodiments, the cartridges may be vertically oriented, suchthat the process fluids are drawn in a generally upwards direction intothe cartridges and leave the cartridges in a generally downwardsdirection. This vertical orientation may serve to preserve space and mayhelp with efficient fluid removal from one or more of the bioprocessingchambers. In some embodiments, the cartridges may have one or moreprocess fluid supplies that do not enter and/or leave the bioprocessingcartridges in a generally vertical orientation. In some embodiments, thecartridges may be horizontally oriented, such that fluid can be pumpedinto and out of the cartridge in a horizontal direction. The fluids maybe contained such that loss of fluid or spillage would be prevented, forexample, by containing the fluid in a closed volume containers which maybe capable of deforming to eject fluid from the container or acceptfluid coming into the container. The fluid may be pumped into thebioprocessing chambers of the cartridge and then aspirated out of thebioprocessing chambers of the cartridge using suction or vacuumpressure. The fluids may be located in the same horizontal plane or in ahorizontal plane parallel to the cartridge or cartridges plane. In someembodiments, the fluid and fluid containers may be oriented in avertical orientation with respect to the cartridge or cartridges whereinthe cartridge or cartridges are in fluid communication with the fluidcontainers through tubing connecting the vertical fluid containers withthe horizontal cartridge or cartridges.

In some embodiments, the device may comprises a removable fluidcontainer tray comprising one set or multiple sets of fluid containerholders able to hold fluid containers for use during bioprocessing. Thenumber of sets of fluid container holders may be any suitable numberaccording to the protocol for which the containers are being used. Insome embodiments, the number of sets of fluid container holders may beequal to or less than the number of slots within the device. In someembodiments, the number of sets of fluid container holders may be morethan the number of slots within the device. In some embodiments, such asembodiments when fewer bioprocessing cartridges than the number of slotsin the machine are being used, blank fluid container holders may beprovided beneath the empty slots.

The fluid container holders may be configured to receive waste, reagentand/or sample containers in appropriate size and number according to thebioprocess to be performed. For example, in some embodiments, the fluidcontainer holders are provided to receive a set of fluid containers,where the set includes at least one sample container, at least onereagent container, and/or at least one waste container. In someembodiments, the fluid container holders may be configured to receivedifferently sized containers each according to their function. Forexample, in some embodiments, the sample container is sized differentlyfrom one or more of the reagent containers, the waste container may alsobe sized differently from either or both the reagent containers and thesample containers, and the reagent containers may each be the same size.In this way, it should be understood that a set of fluid containerholders may comprise multiple differently sized holders for differentlysized containers. In some embodiments, sets of the fluid containerholders are individually pre-packaged with either empty or pre-filledreagent containers and available waste containers and the sets of thefluid container holders may be placed in the removable fluid containertray with the sample container added to the appropriate available fluidcontainer holder by the operator according to a predetermined protocol.In some embodiments, multiple sets of fluid container holders arepre-packaged with either empty or pre-filled reagent containers andavailable waste containers together to fit an entire removable fluidcontainer tray or may be supplied with a removable fluid container tray.In some embodiments, the fluid container holders are configured to shareone or more containers. For example, the fluid container holders may beconfigured to share a waste container or a reagent container. In someembodiments, the fluid container holders and/or the removable fluidcontainer tray are multi-use or single use.

In some embodiments, the bioprocessing device also includes an automatedcontrol system, which includes a computer control system configured tocontrol at least one parameter associated with a bioprocessing procedureor protocol. In some embodiments, the computer control system may beconfigured to control one or more of the following non-limiting examplesof parameters: the actuation of one or more access valves on abioprocessing cartridge; the actuation of one or more pumps on abioprocessing cartridge; the amount of one or more process fluidssupplied to one or more bioprocessing cartridges; mixing of one or moreprocess fluids; exposure time of one or more solid supports to one ormore process fluids, pumping and flow paths of one or more processfluids, circulation of one or more process fluids; pumping flow rates,sequence, pumping delays, and volume of process fluid addition and/orpurging from one or more bioprocessing cartridges and pressure and/orvacuum supplied to the one or more bioprocessing cartridges, such as toone or more control fluid channels on a bioprocessing cartridge.

In some embodiments, the automated control system includes one or moreof the following: a computer control system comprising a centralprocessing unit, a graphical user interface (“GUI”), and an operatorinput system. The central processing unit may include memory and one ormore microcontrollers. In operation, a user may use the operator inputsystem in conjunction with the GUI and software or firmware loaded onthe computer control system to select either one or more storedprotocols or to enter one or more user generated protocols whichinstruct the one or more microcontrollers to initiate a series of valveand pump actuations on one or more bioprocessing cartridges in one ormore slots of the device. The valve and pump actuations may becontrolled using the pressure and vacuum supplies. These valve and pumpactuations may serve to pump process fluids, including reagents andsamples from containers in the fluid container holders into the processfluid channels and bioprocessing chambers of the bioprocessingcartridges and from the bioprocessing cartridges into one or more fluidcontainers and to process the samples according to the selectedprotocol. In some embodiments, the automated control system is able toperform the same or different protocols on multiple bioprocessingcartridges in the device using the same types or different types of setsof fluid container holders, containers, reagents and samples for eachprotocol. During processing, the GUI may provide for the user to observethe progress of the one or more protocols being performed on thebioprocessing cartridges and the computer control system may provide foralarms to indicate completion of the processing or errors or otherproblems that may occur during processing. In some embodiments, thebioprocessing device and/or the computer control system may also includesafety interlocks that prevent the device from running a protocol if thedevice is in one or more unsafe or unprepared states, such as, by way ofnon-limiting example, the container tray is not fully inserted into thedevice, one or more bioprocessing cartridges are not properly insertedinto the slots or are not properly connected to the air and/or vacuumsupply, the air or vacuum supply is inadequate, the air or vacuum supplyexceeds safety limits and/or the electrical supply is inadequate orexceeds safe limits.

The operator input system may comprise any appropriate input system,such as a keyboard, keypad, mouse, touchscreen or any other suitabledevice used by users to interact with computer systems and to runsoftware or firmware. The software or firmware used in the bioprocessingdevice may be application specific or may be commercial off the shelfsoftware. In some embodiments, the bioprocessing device may includesensors for monitoring the progress of one or more protocols running onthe device. For example, the device may include pressure and vacuumsensors for measuring the pressure and vacuum supplied during varioussteps of the protocol, flow rate sensors, temperature sensors, timelapse sensors, sensors for measuring any parameters associated with oneor more steps of processes performed on the device. The sensors mayprovide passive measurement of various parameters that may be recordedin the control system or may provide active measurement that may be usedfor control of the progress and conduct of the process. Such control mayoccur using any suitable control procedure, including, but not limitedto proportional, integral, proportional-integral orproportional-integral-derivative control.

In some embodiments, the computer control system further includesdevices and/or mechanisms for remote control of the device and/or foruploading information into the computer control system such as softwareor firmware updates and for downloading and/or storing informationassociated with one or more runs performed on the device. For example,the device may provide for upload of information onto the device ordownload of the process parameters used for any run directly onto acomputer via a direct connection, such as an ethernet port, a PersonalComputer Memory Card International Association (PCMCIA) slot or anuniversal serial bus (USB) port, via a wireless connection, via aportable storage medium such as a flash drive or thumb drive, a writableCD-ROM, or DVD or the device may be connected to a network, such as aLAN or WAN or to an internet-based application. In addition, the devicemay provide for secure recordation of the process parameters, preventingor ensuring no modification of the actual run parameters after a run hasbeen conducted and may provide for date/time validation of the runs. Insome embodiments, the software or firmware is configured to interfacewith an electronic notebook program, such as a secure electronicnotebook program to download the process parameters and run datadirectly into the program.

In some embodiments, the device is sized to allow for use on a typicallab bench-top or within a chemical hood and may be used at a variety oftemperatures such as at room temperature or in a cold room.

In use, the automated control system verifies that the bioprocessingcartridges are properly inserted into the device, and then may acceptthe user selected protocol (either pre-loaded or user generated). Thebioprocessing device may be pre-programmed with a protocol such as awestern protocol or a nucleic acid purification protocol or a southernprotocol. In some embodiments, the bioprocessing device may be capableof storing additional protocols. The device may allow the user to selectfrom a list of existing protocols or create and save a user definedprotocol, for example, a user defined western or nucleic acidpurification protocol. In some embodiments, the device may further allowfor more consistent and reproducible run-to-run experimentation. Thedevice may also be programmed with a protocol without the need forre-optimization between runs. After the protocol is selected, theautomated control system will actuate the valves and pumps according tothe selected protocol to pump fluids from the fluid containers into thebioprocessing cartridges and bioprocessing chambers therein to performthe desired bioprocessing on the cartridge.

II. BIOPROCESSING CARTRIDGE

In some embodiments, a bioprocessing cartridge may comprise mesofluidicor microfluidic circuits that have been formed from one or moresubstrate layers. In some embodiments, bioprocessing cartridge mayinclude one or more additional layers or elements between the one ormore the substrate layers. In some embodiments that include the one ormore additional layers or elements, at least one of the additionallayers or elements may include one or more membranes or a membrane layerthat may be used in conjunction with the substrate and a pressure orvacuum source as at least one valve or pump.

In some embodiments, the bioprocessing cartridge may comprise at leastone bioprocessing chamber configured to contain a solid support and aplurality of mesoscale and/or microscale fluid flow channels in director indirect fluid communication with the bioprocessing chamber throughat least one pump, such as a pump that is integral or included in,within or on the cartridge or one or more layers from which thecartridge is constructed. In some embodiments, the fluid flow channelsmay comprise process fluid channels and/or control fluid channels. Insome embodiments, the bioprocessing cartridge may comprise two or morefluid layers. In some embodiments, the bioprocessing cartridge mayinclude at least a process fluid layer and a control fluid layer. Insome embodiments, there may be communication between the process fluidlayer and the control fluid layer either directly or indirectly. In someembodiments, the process fluid layer may comprise the layer with themajority of the process fluid channels thereon, while the control fluidlayer may comprise the layer with the majority of the control fluidchannels thereon.

As used herein, the term “microscale” refers to flow channels or otherstructural elements, having at least one cross-sectional dimension onthe order of about 0.1 μm to less than about 1000 μm, such as about 0.1μm to about 500 μm, about 10 μm to about 250 μm or about 100 μm to about250 μm, and the term “mesoscale” refers to flow channels or otherstructural elements, having at least one cross-sectional dimension onthe order of about 1000 μm to about 4 mm, such as about 1000 μm to about3.5 mm, about 1000 μm to about 2.5 mm, about 1000 μm to about 1.5 mm, orgreater than about 1000 μm, greater than about 1100 μm, greater thanabout 1250 μm or greater than about 1500 μm.

In some embodiments, the bioprocessing cartridge may comprise aplurality of mesoscale and/or microscale process fluid flow channels. Insome embodiments, the process fluid flow channels may provide fluidconnection between process fluid connectors on a bioprocessing cartridgeand one or more pumps, access valves and/or process valves on thebioprocessing cartridge. In some embodiments, the process fluid flowchannels may be used to supply process fluids, such as reagents and/orsamples, through the various valves and pumps on a bioprocessingcartridge and into any of one or more bioprocessing chambers on abioprocessing cartridge. In general, the process fluid channels maydirect any of the process fluids, such as reagents and/or samples usedin the actual processes performed on the bioprocessing cartridge, to theappropriate places at the appropriate times. In some embodiments, one ormore of the process fluid flow channels may be provided on a differentfluidic layer than the control fluid flow channels.

In some embodiments, the bioprocessing cartridge may comprise aplurality of mesoscale and/or microscale control fluid flow channels. Insome embodiments, the control fluid flow channels are microscale. Insome embodiments, the control fluid flow channels are mesoscale. In someembodiments, the control fluid flow channels may provide fluidcommunication between control fluid connectors on a bioprocessingcartridge and one or more pumps, access valve and/or process valves onthe bioprocessing cartridge. In some embodiments, the control fluid flowchannels may be used to individually supply pressure or vacuum to themembranes of pumps and valves on the bioprocessing cartridge to actuatethe pumps or open or close the valves. In some embodiments, the controlfluid flow channels may be on a different fluid layer of thebioprocessing cartridge than the process fluid channels.

In some embodiments, the bioprocessing cartridge may be a disposablecartridge. A disposable cartridge may reduce the danger ofcross-contamination between runs. The cartridge may be configured sothat a consistent amount of solution or reagents may be delivered to thecartridge to increase reproducibility.

In some embodiments, the control fluid connectors may be configured toconnect the plurality of control fluid flow channels to an automatedcontrol system. In some embodiments, each of the control fluid flowchannels may be in fluid communication with an independent control fluidconnector. In some embodiments, the control fluid connectors may beconfigured to be in communication with the automated control system viaa control fluid manifold. In some embodiments, the bioprocessingcartridges may be configured to be held in a cartridge holder of abioprocessing device that urges the control fluid connectors into fluidcommunication with supply connectors on the bioprocessing device thatare in fluid communication with a control fluid manifold. In someembodiments, the urging is accomplished using an expanding bladder orsack, a mechanical or manual latching mechanism or an electroniclatching or connecting mechanism, or any other suitable mechanism forurging the control fluid connectors into fluid communication with thesupply connectors.

In some embodiments, the bioprocessing cartridge may comprise one ormultiple bioprocessing chambers, including, but not limited to, onebioprocessing chamber, two bioprocessing chambers, two or morebioprocessing chambers, three bioprocessing chambers, three or morebioprocessing chambers, four bioprocessing chambers, four or morebioprocessing chambers, five bioprocessing chambers or five or morebioprocessing chambers, or any suitable number of bioprocessingchambers. The bioprocessing chambers may be closed or sealed such as byany suitable sealing means including use of gaskets, o-rings, welds,clamps, and the like or, in some embodiments, one or more bioprocessingchambers may be accessible by an operator or user. In some embodiments,the bioprocessing chambers may have inlets and outlets on differentfluidic layers of the bioprocessing cartridge, while in otherembodiments, the bioprocessing chambers may have inlets and outlets onthe same fluidic layers. In some embodiments, the volume of theprocessing chamber should be suitable to allow for fluid to freely flowacross a solid support therein or across the surface of a solid supporttherein. In some embodiments, the bioprocessing chambers may have afluid volume with or without the solid support present of between about1 μl and about 100 ml, such as between about 10 μl and about 100 ml,between about 20 μl and about 100 ml, between about 50 μl and about 100ml, between about 100 μl and about 100 ml, between about 150 μl andabout 100 ml, between about 200 μl and about 100 ml, between about 250μl and about 100 ml, between about 300 μl and about 100 ml, betweenabout 500 μl and about 100 ml, between about 750 μl and about 100 ml,between about 1 ml and about 100 ml, between about 2 ml and about 75 ml,between about 3 ml and about 60 ml, between about 4 ml and about 50 ml,between about 4 ml and about 45 ml, between about 4 ml and about 40 ml,between about 4 ml and about 35 ml, between about 5 ml and about 30 ml,between about 10 ml and about 25 ml or between about 15 ml and about 20ml.

The bioprocessing chambers may comprise fluid mixing chambers and/or maycontain a solid support for processing one or more samples. The solidsupport can be any support for filtering, washing, staining, eluting,collecting, processing or conducting chemical reactions orbioprocessing. In some embodiments, the solid support may be selectedfrom one or more of the following: filter cassettes, filter paper,precipitation membranes, precipitation filters, solid phase extractioncolumns, solid phase extraction cassettes, solid phase extraction disks,resins, membranes, such as blotting membranes, filter membranes, PVDFmembranes, nylon membranes, positively charged nylon membranes andnitrocellulose membranes, reaction beads, such as glass beads andmagnetic beads, rigid planar solid supports that contain arrays ofbiomolecules such as nucleic acid microarrays, protein arrays, andtissue arrays, microscopic slides and combinations thereof.

In some embodiments, the solid support in one or more bioprocessingchambers may comprise a filter paper, a filter or a filter cassette. Thefilter paper, filter or filter cassette may comprise any suitable typeof filter having an appropriate chemistry, pore size, shape and threedimensional configuration, such as a symmetrical or asymmetrical threedimensional configurations including “V” or funnel-shaped poreconfigurations, and surface area for the intended use and maybeconstructed for flow through, cross flow, tangential flow or anycombination thereof. The filter paper, filter or cassette may compriseany suitable material, such as poylethersulfone, polyethylene,ultra-high molecular weight polyethylene, polypropylene, nylon,cellulose, cellulose-triacetate, polyacrylonitrile, polyamides, glassfiber, silica, polysulfone, PVDF, and the like. In some embodiments, thesolid support in one or more processing chambers may comprise aprecipitation membrane or a precipitation filter. In some embodiments,the solid support in one or more processing chambers may comprise asolid phase extraction column, a solid phase extraction cassette or asolid phase extraction disk. In some embodiments, the solid support inone or more processing chambers may comprise a blotting membrane. Thefilter, filter paper, or filter cassette may be a single layer ormultiple layer filter. In some embodiments, the solid support in one ormore bioprocessing chambers may comprise a plurality of beads such ascoated beads, coated glass beads, glass beads, magnetic beads or coatedmagnetic beads.

In some embodiments, the bioprocessing chambers are open and provideaccess to the user for insertion of a solid support. In someembodiments, the bioprocessing chambers are open and are configured toreceive a blot membrane with or without a blot membrane holder. Blotmembrane holders may be used to prevent the blot membrane fromcontacting or sticking to one of the faces of the bioprocessing chamberand may be used to facilitate flow of the various process fluids aroundand across the surfaces of the blot membrane. In addition, in someembodiments, the bioprocessing chambers may include additional space toaccommodate foaming during processing of a sample. For example, in someembodiments, where the bioprocessing chamber is open and a blot membraneis inserted by a user with or without a blot membrane holder, thebioprocessing chamber may be sized to provide additional space at thetop of the chamber to prevent overflow of foam that may be formed duringthe bioprocessing. In addition, the bioprocessing chamber may beconfigured at the top such that the chamber is wider at the top than atthe bottom. This increased width at the top provides additional volumeto accommodate foam formation, if present.

In some embodiments, the bioprocessing cartridge may include one or moreflow control elements. In some embodiments, the one or more flow controlelements may be selected from pumps, process valves, check valves,access valves, layer pass-throughs and/or pass-through valves. In someembodiments, one or more of the flow control elements may be placedwithin a flow path defined by one or more of the plurality of fluid flowchannels on the bioprocessing cartridges.

In some embodiments, the bioprocessing cartridge may comprise from about1 to about 10 pumps, such as from about 1 to about 8 pumps, from about 1to about 6 pumps, from about 1 to about 5 pumps or from about 1 to about4 pumps. The pumps may be included in, within, or on, or may be integralto the bioprocessing cartridges or at least one layer of thebioprocessing cartridges. The pumps may be used to pump process fluidsfrom process fluid containers into or out of the cartridges and throughthe plurality of process fluid channels on the cartridges. In someembodiments, a pump may be actuated by providing pressure and/or vacuumto the membrane of the pump using a control fluid channel associatedwith the pump on a different fluidic layer than the process fluidchannels associated with the pump. In this manner the pumps may comprisemembrane pumps similar to diaphragm pumps. In some embodiments, thepumps, when actuated may cause the fluid flow in the process channels tobe turbulent, while in other embodiments, the fluid flow in the channelsmay be laminar or transitional.

In some embodiments, the bioprocessing cartridge may comprise from about1 to about 20 access valves, such as from about 2 to about 18 from about3 to about 16, from about 4 to about 14, from about 5 to about 13, fromabout 6 to about 12 or from about 7 to about 10 access valves. In someembodiments, the access valves control access of process fluids to andfrom the bioprocessing cartridges and generally are in direct fluidcommunication with one or more process fluid connectors on thebioprocessing cartridge. In some embodiments, the access valves may beactuated to open or close by providing pressure or vacuum to themembrane of the access valve using a control fluid channel associatedwith the access valve on a different fluidic layer than the processfluid channels associated with the valve, thereby opening or closingfluid communication between at least one process fluid channel on thebioprocessing cartridge and the process fluid connectors on thebioprocessing cartridge. When closed, the access valves may preventprocess fluid from flowing into or out of the bioprocessing cartridge.In some embodiments, the bioprocessing cartridge may comprise an accessvalve within each of the flow paths between the process fluid connectorsand each of the plurality of fluid flow channels. In some embodiments,at least two of the plurality of process fluid connectors share anaccess valve.

In some embodiments, the bioprocessing cartridge may comprise from about1 to about 25 process valves, such as from about 1 to about 22, fromabout 1 to about 20, from about 1 to about 18, from about 2 to about 16,from about 2 to about 14, from about 3 to about 12, from about 3 toabout 10 or from about 3 to about 8 process valves. The process valvesmay be either actuated to open or actuated to close depending on theindividual process. In some embodiments, a process valve may be actuatedby providing pressure or vacuum being supplied to the process valvemembrane via a control fluid channel on a different fluidic layer thanthe process fluid channels associated with the process valve. Theprocess valves may be used to route fluids to the appropriate places onthe bioprocessing cartridges according to the protocols at theappropriate times after the fluids have accessed the bioprocessingcartridges through one or more access valves. In some embodiments, thebioprocessing cartridges comprise at least one process valve in a flowpath between a pump and a bioprocessing chamber.

In some embodiments, the bioprocessing cartridge may include a checkvalve. In some embodiments, the bioprocessing cartridge may comprise atleast one check valve. In some embodiments, the check valve or valvesmay allow for flow through the valve in one direction only, includingflow between layers and may be actuated to open for flow in thatdirection via pressure supplied to the valve membrane via a controlfluid channel or via pressure associated with process fluid flowing inthe flow channel in the correct direction. In some embodiments, checkvalves may be provided to supply a control fluid between two differentlayers of a bioprocessing cartridge. In some embodiments, the controlfluid may be supplied to serve as a process fluid, such as to provideair pressure for drying a filter or membrane or to expel residual fluidsin a pump, channel or bioprocessing chamber. In some embodiments, thecheck valves may allow for fluid to flow across them in one directionand fluid to flow in one direction through them between layers. In someembodiments, check valves are provided that allow for flow in eitherdirection across them, but that allow for flow through them in only onedirection, such as in one direction either from the process fluid layerto the control fluid layer or from the control fluid layer to theprocess fluid layer on a bioprocessing cartridge. In some embodiments,the bioprocessing cartridges comprise at least one check valve that is aprocess valve or an access valve.

In some embodiments, the bioprocessing cartridge may include at leastone layer-pass through or pass-through valve. The layer pass-throughs orpass-through valves may provide for flow of a process fluid betweendifferent fluidic layers on a bioprocessing cartridge. For example,where the inlet to a bioprocessing chamber is on a different fluidiclayer than a given flow channel associated with fluid intended for thechamber, the flow channel may direct the fluid to a layer pass-throughor a pass-through valve where the fluid is transferred from one fluidiclayer to the fluidic layer associated with the inlet to the processingchamber and may then proceed into the processing chamber via processfluid channels on the other fluidic layer. Layer pass-throughs generallyare passive fluidic connections between fluidic layers, whilepass-through valves may control the flow of the fluid from one layer toanother by requiring actuation to either open or close either by thepressure in the fluid channel itself or by actuation using a controlfluid.

In some embodiments, the bioprocessing cartridge includes one or moreprocess fluid connectors. In some embodiments, the process fluidconnector may include tubes or tube-like structures that are configuredto fluidly connect the cartridge to one or more outside (i.e. not on thebioprocessing cartridge) fluid containers. Fluids may be introduced intothe cartridge or removed from the cartridge and from or into the one ormore fluid containers through the process fluid connectors, and thentransported through the fluid flow channels into the various portions ofthe bioprocessing cartridge. In some embodiments, the bioprocessingcartridge or cartridges may include between about 3 to about 20 processfluid connectors, such as about 4 to about 18, about 5 to about 16,about 6 to about 14, or about 8 to about 12 process fluid connectors, orabout 3 or more process fluid connectors, about 4 or more process fluidconnectors, about 5 or more process fluid connectors, or about 6 or moreprocess fluid connectors. In some embodiments, the process fluidconnectors are connected to a process fluid manifold on a bioprocessingdevice through which the various process fluids may be supplied to andremoved from the bioprocessing cartridge via one or more of theplurality of flow channels. In some embodiments, each of the processfluid connectors receives fluid from an independent fluid container,where each container may contain the same or different fluids as inanother container.

In some embodiments, the process fluid connectors may be in fluidcommunication with the process fluid reservoirs viaaspiration/expiration tubes, which may be in fluid communication withthe process fluid connectors or the process fluid connectors may beaspiration/expiration tubes. When placed in a slot of a bioprocessingdevice, the aspiration/expiration tubes may extend away from thecartridge and into the fluid reservoirs. In one embodiment, theaspiration/expiration tubes may extend into reservoirs positioned belowthe cartridge slot when the cartridge is inserted into the cartridgeslot. The reservoirs may be any tube, bottle, vial or similar reservoirable to hold a fluid. In some embodiments, the reservoirs may include asealing layer that may permit the tips of the aspiration/expirationtubes to pass into the reservoirs but which may also reduce the risk ofan external substance from entering the reservoirs, or which may reducesthe loss of reagents or fluids from the reservoirs. Theaspiration/expiration tubes may have the same or different lengths withrespect to each other, depending on the size and/or shape of thereservoir or reservoirs. While the aspiration/expiration tubes may beused to transport process fluid from a reservoir into the cartridge, theaspiration/expiration tubes may also be used to expel fluids as wastefrom the cartridge into one or more of the reservoirs.

In addition, in some embodiments, the containers in conjunction with theaspiration/expiration tubes and the bioprocessing cartridge orcartridges may be used to receive one or more containers or mixingcontainers for process fluids during bioprocessing. For example, in someembodiments, fluid may be removed from one process fluid container intothe bioprocessing cartridge and then out of the bioprocessing cartridgeand into a different container. In this manner the fluid may be pumpedback and forth between the containers using the bioprocessing cartridgeto provide mixing of the fluids. Alternatively, in some embodiments,fluids may be removed from and returned back to the same container toprovide mixing of the fluid without combining it with any other fluids.Furthermore, in some embodiments, one or more of the containers and thecontainer holder or holders, the container tray and the bioprocessingdevice may be configured to provide stirring of a fluid in thecontainer, such as, for example, a magnetic stirring rod, or any othersuitable stirring mechanism for stirring or agitating a fluid in thecontainer.

In some embodiments, the bioprocessing cartridge may include one or morepre-loaded or on-board process fluids or process reagents. In suchembodiments, the process fluids or process reagents may be included inseparate reservoirs or chambers on the cartridge or may be included inone or more pumps or channels on the cartridge. In some embodiments, thepre-loaded or on-board process fluids or process reagents may comprise aprocess fluid or a component of a process fluid. In some embodiments,the pre-loaded or on-board process fluids or process reagents maycomprise a process reagent that is dissolved into a process fluid afterexposure to the process fluid.

In some embodiments, the bioprocessing cartridge may be designed formultiple uses. In some embodiments, the cartridge may be disposableand/or designed for a specific or limited number of uses, such as about20 uses or less, about 15 uses or less, about 10 uses or less, about 9uses or less, about 7 uses or less, about 5 uses or less, or about 3uses or less. In some embodiments, protocols may be provided on theautomated control system to provide for cleaning of the multiple usecartridge prior to re-use. Accordingly in some embodiments, thecartridge may be a consumable product.

In some embodiments, the bioprocessing cartridges may be single usecartridges. In some embodiments, the cartridge may include an indicatorconfigured to signal when a cartridge has and/or has not been used. Insome embodiments, the indicator may be any suitable indicator forindicating when a cartridge has and/or has not been used. In someembodiments, the indicator may be a color indicator located on the cardat a suitable location, such as in a color indicator chamber, whichcolor indicator may permanently change color during bioprocessing toindicate that the cartridge has been used. In some embodiments, theautomated control system of a bioprocessing device may be configured todetect the color change and prevent operation when a used card is placedin a slot. In some embodiments, the automated control system of abioprocessing device may be configured to detect both the indicatorcolor prior to the color change and after the color change and mayprevent or stop operation when one or both of the colors are notobserved at different times.

In some embodiments, the indicator may include, a bibulous matrix, suchas a white bibulous matrix such as a paper tape that is impregnated onone side with a red dye while the other side is white such that whenthat matrix is wetted, the dye diffuses throughout the matrix, turningthe side that was white to a red color. In some embodiments, the whiteside is initially displayed to the device's detector. The detector maythen view the change in the indicator from white to red when a cartridgehas been used. In some embodiments, the color change may be produced bydirecting some of the liquid used in the bioprocessing device to aseparate chamber containing a piece of color indicator tape. The tapemay remain wetted by including a check valve that permits fluid flowinto the tape chamber but prevents the fluid from returning to theprocess fluid channel after it has interacted with the dye. In addition,once the indicator material has been wetted and the dye redistributedthroughout the matrix, thereby turning the white side red, the colorremains in the matrix even after the matrix dries out. An example of asuitable color indicator tape is described in U.S. Pat. No. 7,105,225the entire contents of which are hereby incorporated by reference. Inaddition, suitable indicator tapes may include water contact indicatortapes such as 3M® Water Contact Indicator Tapes 5557, 5558, or 5559.

In some embodiments, the water sensitive paper or tape may comprise asmall round piece of paper or tape (approx 5-15 mm, such as 8 mm indiameter) positioned between two layers of a bioprocessing cartridge andwithin a chamber that allows it to be clearly viewed by the customerwhen the card is out of the instrument and by an electronic color sensorwhile the cartridge is inserted within the instrument. When thecartridge is used during a run, a small portion of the first liquid toenter the cartridge enters the chamber containing the paper or tape,causing the color change. This change may occur after less than about 20seconds of run time. An electronic color sensor, such as a color sensorwith integrated LED illumination may be imbedded in the bioprocessingdevice, such as in the cartridge slot. When running a protocol, afterthe “Run” button is pushed by the user, the color sensor detects thecolor of the paper or tape and may send an input to the GUI that willdirect the user to insert a new card if the incorrect color is detected.In some embodiments, the system may also allow for a second colordetection during a run. In some embodiments, the second color detectioncan occur as follows: the GUI interrogates the sensor again after a setlength of run time has occurred, such as between about 1 minute andabout 10 minutes, such as about 2 minutes or more, about 3 minutes ormore, about 4 minutes or more or about 5 minutes or more, to determineif the paper or tape has changed color. If the paper or tape has not, anerror message is displayed and the protocol is stopped.

In some embodiments, the color sensor may determine a color change asfollows. At calibration, each sensor may output a signal in response toa standard red card and a standard white card. The midpoint betweenthose signals (in kHz) is determined to be the dividing point betweenwhat is considered red (used) and what is considered white (unused).This information may be permanently saved within the instrument memory.In operation by a user, this information is used for the first colordetection as described above. For the second test, another check is madeafter the set time period, such as after 2 minutes into the run and thereturned value compared to the first. If there is a change of 1 kHz ormore, the card is determined to have not been tampered with and the runcontinues. If this change is not detected, the run can be stopped andthe user instructed to insert a new cartridge or cartridges.

In some embodiments, the color sensor may determine a color change asfollows. During the calibration period a series of measurements aretaken at set time intervals to establish a baseline color level. Afterthe calibration period, measurements of the color are taken at set timepoints. Each measurement is compared to the baseline level. Once a colorlevel is detected that is more than about 2 standard deviations, morethan about 3 standard deviations, more than about 4 standard deviations,or more than about 5 standard deviations from the base line color level,a color change is deemed to have occurred and the card is deemed to havenot been tampered with and the run continues. If a color change asdetermined by an appropriate number of standard deviations has notoccurred, the run can be stopped and the user instructed to insert a newcartridge or cartridges.

In some embodiments, the bioprocessing cartridge may include one or morepumps, valves, process fluid channels and/or control fluid channels thatare integral to the cartridge, such as included on one or more layers ofthe cartridge. In some embodiments, the process fluid channels and/orthe control fluid channels are rigid flow channels or have one or morerigid walls. The channels may be any suitable cross-sectional shape,including circular, elliptical, square, rectangular, D-shaped and anyother suitable polygonal cross-section. In some embodiments, one or moreof the channels may have a D-shaped cross-section or a square orrectangular shaped cross-section, where the substantially-semicircularportion of the channel (for D-shaped cross-section) or three sides ofthe channel (for the square or rectangular cross-section) has rigidwalls and where the flat portion of the channel (D-Shape) or the fourthside of the channel is formed from a film that may be the same or adifferent material from the rigid walls and that may be flexible or lessrigid than the material used for the rigid walls or more rigid than thematerial used for the rigid walls. In some embodiments, the flexible orless rigid material is flexible or less rigid as a result of itsthinness, rather than as a result of the inherent material properties ofthe flexible or less rigid material. For example, in some embodiments,one or more of the process fluid channels or control fluid channels mayhave a D-shaped or square or rectangular cross-section, where the flatside (D-shaped) or one of the sides (square or rectangular-shapedcross-section) of one or more of the channels comprises a metal orplastic film or foil and the other side or sides of the one or morechannels comprise plastic. In some embodiments the process fluidchannels and/or the control fluid channels are not flexible tubing.

In some embodiments, the bioprocessing cartridges may be regularlyshaped, such as rectangular, square or generally rectangular orgenerally square, while in other embodiments, the bioprocessingcartridges may have more complex polygonal shapes or be generallypolygonal in shape or be irregularly shaped. In some embodiments, thecartridges may have at least one dimension that is longer than about 5cm, such as at least one dimension that is between about 6 cm and about40 cm, such as between about 7 cm and about 37 cm, between about 8 cmand about 35 cm, between about 9 cm and about 30 cm, between about 10 cmand about 25 cm, between about 11 cm and about 22 cm, between about 12cm and about 21.5 cm, between about 12 cm and about 20 cm, between about12 cm and about 18.5 cm, between about 14 cm and about 18.5 cm,excluding any addition to the dimensions of the bioprocessing cartridgesas a result of protrusions, including but not limited to protrusionssuch as process fluid connectors, control fluid connectors andaspiration/expiration tubes. In some embodiments, the bioprocessingcartridges may be generally flat, having at least one dimension(“depth”) that is substantially shorter than one or both of the otherdimensions. In some embodiments, the bioprocessing cartridges have adepth that is less than about 50% of the longest dimension as measuredabove, such as less than about 40% of the longest dimension, less thanabout 30% of the longest dimension, less than about 25% of the longestdimension, less than about 20% of the longest dimension, less than about15% of the longest dimension, less than about 10% of the longestdimension or less than about 7.5% of the longest dimension.

In some embodiments, the bioprocessing cartridges may include one ormore cartridge alignment guides to ensure the cartridge is inserted inthe proper orientation into the cartridge slot. In some embodiments, thecartridge alignment guide may be a tab or tabs or a projection orprojections, or groove or grooves that fit within a correspondingopening in the cartridge slot as the cartridge is inserted into thecartridge slot.

III. METHODS OF BIOPROCESSING

In some embodiments, methods of bioprocessing include: providing abioprocessing cartridge, where the cartridge comprises at least onebioprocessing chamber containing a solid support and a plurality ofmesoscale and/or microscale fluid flow channels in fluid communicationwith the bioprocessing chamber; and pumping at least one process fluidthrough at least one of the plurality of channels into the at least onebioprocessing chamber. In some embodiments, the pumping includes pumpingone or more process fluids and/or a sample into said processing chamberand into contact with the solid support. The process fluids delivered tothe solid support in the cartridge may be any suitable solvent, solutionor reagent for use in the desired bioprocess, including but not limitedto liquid reagents used for chemical reactions, solvents or solutionsused for washing, antibody solutions, buffer solutions, blocking buffersolutions and solutions containing fluorescent labeling reagents. Theprocess fluids also may include samples that are to be processed such asproteins, nucleic acids and other macromolecules, cells, cell lysates,and combinations thereof. In some embodiments, the at least oneprocessing fluid includes at least one blocking buffer. In someembodiments, the at least one processing fluid includes at least oneantibody. In some embodiments, the at least one processing fluidincludes at least one washing fluid. In some embodiments, the method ofbioprocessing may include pretreating the cells prior to pumping. Insome embodiments, pretreating the cells may include adding a salt to thecells, such as for example, NaCl, MgCl₂, CaCl₂, NH₄Cl and the like. Thecells may be pretreated using any suitable method for pretreating cellsto increase plasmid yield. In some embodiments, the salt solutionconcentration may be any suitable concentration for improving yield, forexample, a concentration of between about 0.1M and about 0.5M, betweenabout 0.2M and about 0.5M. In some embodiments, the salt concentrationmay be any suitable concentration for increasing the plasmid yield by atleast 20%, by at least 30%, by at least 40%, by at least 50%, by atleast 55%, by at least 65%.

In some embodiments, the pumping at least one process fluid through atleast one of the plurality of channels into the at least onebioprocessing chamber includes pumping the at least one process fluidthrough a flow channel accessing the bottom portion of the chamber. Insome embodiments, the pumping at least one process fluid through atleast one of the plurality of channels into the at least onebioprocessing chamber includes pumping the at least one process fluidthrough a flow channel accessing the top portion of the chamber. In someembodiments, the pumping at least one process fluid through at least oneof the plurality of channels into the at least one bioprocessing chamberincludes pumping the at least one process fluid through a flow channelaccessing a side portion of the chamber.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes circulating at least one process fluid from thebioprocessing chamber through a fluid flow channel accessing the bottomportion of the chamber, and back into the chamber through a fluid flowchannel accessing an upper portion of the chamber.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes circulating at least one process fluid from thebioprocessing chamber through a fluid flow channel accessing the topportion of the chamber, and back into the chamber through a fluid flowchannel accessing the bottom upper portion of the chamber.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes circulating at least one process fluid from thebioprocessing chamber through a fluid flow channel accessing the sideportion of the chamber, and back into the chamber through a fluid flowchannel accessing a bottom portion of the chamber.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes pumping at least one processing fluid through a filteror filter membrane in the at least one bioprocessing chamber. In someembodiments, the filter membrane comprises a blot membrane. In someembodiments, the filter membrane comprises a western blot membrane. Insome embodiments, the filter comprises a cell separation or cell capturemembrane. In some embodiments, the filter comprises a lysateclarification filter. In some embodiments, the filter comprises anucleic acid precipitate filter. In some embodiments, the filtercomprises a nucleic acid purification filter. In some embodiments, oneor more of the filter membranes or one or more layers of the filtermembranes have at least one pore size that is between about 0.2 μm andabout 3 μm, between about 0.45 μm and about 2.5 μm, between about 0.5 μmand about 2.4 μm, between about 0.65 μm and about 2.2 μm, between about0.8 μm and about 2.0 μm, between about 1.0 μm and about 1.5 μm, orbetween about 1.2 μm and about 1.5 μm. In some embodiments, the filtermembrane comprises a cell separation or capture filter having twolayers, one layer having a pore size between about 1.0 μm and about 1.5μm, such as about 1.2 μm, and one layer having a pore size between about0.5 μm and about 0.8 μm, such as about 0.65 μm. In some embodiments, thefilter membrane may include a nucleic acid precipitation filter havingtwo layers, one layer having a pore size between about 1.0 μm and about1.5 μm, such as about 1.2, μm and one layer having a pore size betweenabout 0.5 μm and about 0.8 μm, such as about 0.65 μm. In someembodiments, the filter membrane may include a cell separation orcapture filter or a nucleic acid precipitation filter which may includean asymmetric filter having a pore size ranging from about 0.65 μm toabout 2 μm. In some embodiments, the filter may include a glass fiberlysate clarification filter having a pore size between about 0.8 μm andabout 1.5 μm, such as about 1.0 μm.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes adding a blocking buffer to the bioprocessing chamber,recirculating the blocking buffer across the surface of a blot membraneto form a blocked blot membrane, adding at least one antibody solutionto the bioprocessing chamber; and recirculating the at least oneantibody solution across the surface of said blocked blot membrane. Insome embodiments, recirculating at least one antibody solution acrossthe surface of the blocked blot membrane may include recirculating aprimary antibody solution across the surface of said blocked blotmembrane; washing the blot membrane; adding a secondary antibodysolution to the bioprocessing chamber; and recirculating the secondaryantibody solution across the surface of the washed blot membrane.

In some embodiments, the action of pumping may provide additional mixingwithin the bioprocessing chamber. For example, in some embodiments,where process fluid is circulated or recirculated through a fluid flowchannel accessing the top or a side portion of the chamber, and backinto the chamber through a fluid flow channel accessing a bottom portionof the chamber, the pressure associated with the pumping action into orback into the chamber may create localized eddy formation or theformation of areas of turbulence that promote flow of the process fluidacross the bioprocessing chamber and mixing of the process fluid withinthe chamber. In some embodiments, when such a pumping method is used inthe presence of a blot membrane with or without a blot membrane holder,the pumping action may serve to move the blot membrane within thebioprocessing chamber slightly with each pumping cycle, serving toensure that the blot membrane is exposed on all sides to the processfluid in a substantially uniform manner and to prevent the blot membranefrom sticking to a surface of the bioprocessing chamber or the blotmembrane holder.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes pumping at least one processing fluid through at leastone solid phase extraction column, at least one solid phase extractionmembrane, at least one solid phase extraction cassette or at least onesolid phase extraction disk in at least one bioprocessing chamber. Insome embodiments, the solid phase extraction column, solid phaseextraction membrane, solid phase extraction cassette or solid phaseextraction disk comprises a silica reversible binding ligand or acharge-switch binding ligand.

In some embodiments, pumping at least one process fluid through at leastone of the plurality of channels into the at least one bioprocessingchamber includes pumping cell culture media or cells suspended in asolution across a cell separation filter to separate cells from the cellculture media, wherein the cells are captured on the filter. In someembodiments, the pumping may further include resuspending the capturedcells in a lysing solution to form a lysate; neutralizing the lysate;and clarifying the lysate. The cells may be resuspended in the lysingsolution and lysed in the chamber or the lysing solution or anothersolution may be used to resuspend the cells and pump them into acontainer, such as a reagent container containing lysing solution, wherethe cells may be lysed. In some embodiments, the lysate may be clarifiedby pumping the lysate through a filter membrane to remove unwantedcellular molecules and debris.

In some embodiments, pumping at least one processing fluid through atleast one of the plurality of channels into the at least onebioprocessing chamber may further include extracting at least onebiomolecule onto a solid phase extraction membrane or disk or cassettein a bioprocessing chamber; washing the solid phase binding material;and eluting the biomolecule from the solid phase. In some embodiments,pumping at least one processing fluid through at least one of theplurality of channels into the at least one bioprocessing chamberfurther includes precipitating and collecting the biomolecule in abioprocessing chamber containing a precipitation filter

In some embodiments, a method of bioprocessing may include: a) insertingat least one bioprocessing cartridge into a bioprocessing device, thebioprocessing cartridge comprising: i) at least one bioprocessingchamber containing a solid support therein; and ii) a plurality ofmesoscale and/or microscale channels in fluid connection with thebioprocessing chamber; b) initiating a bioprocessing protocol on thebioprocessing device, the protocol comprising one or more of thefollowing: i) controlling pumps and valves on the bioprocessingcartridge to supply reagents and/or samples from one or more containersto the at least one bioprocessing chamber of each of the at least onebioprocessing cartridges, ii) controlling pumps and valves on thebioprocessing cartridge to recirculate the reagents and or samplesacross the at least one bioprocessing chamber of each of the at leastone bioprocessing cartridges; and/or iii) controlling pumps and valveson the bioprocessing cartridge to remove reagents and/or samples fromthe at least one bioprocessing chamber of each of the at least onebioprocessing cartridges.

In some embodiments, a method of applying one or more fluids to a solidsupport may include: a) inserting at least one bioprocessing cartridgeinto a bioprocessing device, the bioprocessing cartridge comprising: i)at least one bioprocessing chamber containing a solid support therein;and ii) a plurality of mesoscale and/or microscale channels in fluidconnection with to said bioprocessing chamber; and b) performing apumping sequence on the cartridge, wherein the pumping sequence includesentering one or more fluid addition cycles wherein fluid is pumped fromthe one or more containers within the bioprocessing device through oneof the fluid flow channels and into the chamber.

In some embodiments, the pumping sequence may further include entering apurging cycle following each fluid addition cycle, the purge cycleincluding pumping fluid within the bioprocessing chamber into adesignated waste container. In some embodiments, the pumping sequencemay further include entering a circulating cycle after any of the fluidaddition cycles, wherein the circulating cycle includes opening a valvein a fluid flow channel connected to the bottom of a bioprocessingchamber and pumping fluid from the bottom portion of the chamber throughone or more fluid flow channels and into a top portion of the chamber.In some embodiments, the pumping sequence may be initiated andterminated using a programmable controller.

In some embodiments, a pumping sequence is performed including enteringone or more fluid addition cycles wherein fluid is pumped from containerin fluid communication with one of the process fluid connectors and intothe chamber. The fluid in any of the containers or added during any ofthe fluid addition cycles can be the same or different than fluid in anyof the other containers or added during any other of the fluid additioncycles. The pumping sequence may further include performing a purgingcycle following any of the fluid addition cycles where fluid within thechamber is pumped out of the chamber into a waste container or acontainer designated to collect waste fluid. In some embodiments, fluidfrom multiple reservoirs may be added during the same fluid additioncycle, or a subsequent fluid addition cycle is performed withoutperforming a purging cycle so that two or more fluids may be introducedto a chamber at the same time (although the total volume of the addedfluids cannot exceed the available volume within the chamber). Thepumping sequence may further include entering a circulating cycle afterany of the fluid addition cycles where fluid in the chamber is pumpedfrom the chamber through one or more process fluid channels of thecartridge and back into the chamber.

In some embodiments, the fluid addition cycles may be terminated after apredetermined amount of time elapses or after a predetermined volume offluid is added. Similarly, the purging cycles and circulating cycles maybe terminated after a predetermined time elapses. The amount of timeelapsed and/or the amount of fluid added may vary depending on theselected protocol or type of bioprocessing. In some embodiments, theprotocol may include at least one circulation or incubation cycle, wherethe solid support is exposed to one or more process fluids for aselected period of time either with the fluid circulating or for a holdperiod without fluid circulating.

In some embodiments, the pumping sequence may be designed for theimmunolabeling, rinsing and incubation for a western blot analysis. Insuch embodiments, a blot membrane, such as by way of example anitrocellulose or polyvinylidene fluoride (PVDF) membrane, containingthe separated proteins is placed in the cartridge chamber using amembrane holder that provides for flow of fluid across the chamber andmembrane without allowing the membrane to stick to any of the walls ofthe chamber, and the cartridge is placed in the bioprocessing device.Antibody solutions may be added from the fluid containers in thebioprocessing device to the cartridges and the chamber containing themembrane along with the appropriate blocking and washing solutions. Thepumping sequence, duration, and solutions used are selected depending onthe specific analysis and proteins involved and can be modified by theuser.

In some embodiments, the pumping sequence may be designed for thelabeling of a molecule for a western blot analysis using a label or tag,such as a fluorescent tag, such as quantum dots or fluorescence dyes,such as Alexa Fluor® dyes. Solutions containing labels may be added fromthe fluid containers in the bioprocessing device to the cartridges. Thepumping sequence, duration, and solutions used are selected depending onthe specific analysis and proteins involved and can be modified by theuser.

In another embodiment, the pumping sequence may be designed fortransfection grade plasmid preparations. Bacterial cells in a solutionor in cell culture media are placed in a sample container in thebioprocessing device containing an appropriate bioprocessing cartridge.The cells are captured on a filter by pumping them across a filter in acartridge chamber using the device. The cells are resuspended and lysedusing a lysing solution, such as one or more alkaline solutions, thelysate is clarified by pumping the lysate across another filter in adifferent cartridge chamber. The clarified lysate is passed through asolid phase extraction disk and then to a waste container. The solidphase extraction disk is washed at least once and then the boundbiomolecules are eluted from the solid phase extraction disk. The elutedbiomolecules are captured on a precipitate filter and washed at leastonce, at which point the precipitated biomolecules are dissolved in anappropriate buffer and pumped into a final product container in thebioprocessing device.

In another embodiment, the pumping sequence may be designed for foodsafety analysis. A sample may be placed in a sample container in thebioprocessing device containing an appropriate bioprocessing cartridge.Bacterial cells may be separated from larger debris and are captured ona filter by pumping them across a filter in a cartridge chamber usingthe device. The bacteria may be lysed using a lysing solution, thelysate may be clarified by pumping the lysate across another filter in adifferent cartridge chamber. The clarified lysate may be passed througha solid phase extraction disk and then to a waste container. The solidphase extraction disk may be washed at least once and then the bound DNAare eluted from the solid phase extraction disk and pumped into a finalproduct container in the bioprocessing device.

In some embodiments, a method of applying one or more fluids to a solidsupport may further include independently opening and closing accessvalves connecting to process fluid connectors to selectively control theamount of fluid entering or leaving the fluid flow channels. In someembodiments a method of applying one or more fluids to a solid supportfurther comprises inserting multiple cartridges into the cartridge slotsand performing a pumping sequence on each of the cartridges, where thepumping sequence performed on each cartridge is the same or differentthan the pumping sequence performed on any other cartridge. In someembodiments, the pumping sequences performed on each of the cartridgesare performed at the same time.

In some embodiments, any of the methods of bioprocessing describedherein may be stored as a portion of or as a complete bioprocessingprotocol on a bioprocessing device. In some embodiments, the storedprotocol may further include details delineating timing for each stepand the sequence of opening and closing of valves and pumping of pumpson a bioprocessing cartridge.

In some embodiments, the bioprocessing device and cartridges may be usedas follows: the bioprocessing device is turned on and the variouspressure and vacuum connections and supplies may be checked, one or moresamples to be analyzed or bioprocessed are inserted into one or morefluid container holders along with reagents in reagent containers andwaste containers as necessary. The one or more fluid container holdersare placed in the removable fluid container tray and the tray is pushedinto the bioprocessing device. One or more bioprocessing cartridges isinserted into the slots of the bioprocessing device and placed in fluidcommunication with the fluid containers in the fluid container holders.This fluid communication may be accomplished via a fluid manifold ineach slot or may be accomplished by inserting aspiration/expirationtubes connected to each bioprocessing cartridge into the fluidcontainers. The slots hold the cartridges in place and the control fluidmanifold is connected to the cartridges by inflating bladders within theslots that urge supply connectors on the manifolds to engage controlfluid connectors on the cartridges. The device performs a systems checkto verify that there are no safety issues or connection errors. Usingthe GUI and an input system, an operator selects a bioprocessingprotocol from a menu of stored protocols or may enter a protocol intothe automated control system of the device. The protocol selected orentered includes instructions for controlling pumps and valves on thebioprocessing cartridges to perform the steps of one or morebioprocessing procedures. After completion of the procedure, the devicemay provide an alarm or signal for notifying the operator that theprocedure is complete. The cartridges may be removed from the device anddisposed of and the fluid containers and fluid container holders may beremoved with the removable fluid tray and cleaned and/or disposed of asnecessary.

It should be understood that the above process may be modified,including having one or more steps removed, added or the order of one ormore steps changed without departing from the scope of the methodsdescribed herein.

Referring to FIG. 1A, in some embodiments, a bioprocessing device 100has a housing 10 which may be constructed from any suitable material,such as plastics, metals, composite materials, or any combinationthereof, and which is designed to house the various components of thedevice. In some embodiments, housing 10 may include a sheet metalchassis that is covered with a plastic cover. The sheet metal chassismay be any suitable sheet metal, such as an aluminum sheet chassis,which may provide for structural integrity to the instrument, may limitEMI emissions and may serve as a heat sink for the power supply. Theplastic cover may be constructed from any suitable plastic, such asurethane, and may provide basic protection for the internal componentsand an easy to clean surface. Housing 10 includes openings 17 for accessto slots 13 within the device.

As shown in FIG. 1A, in some embodiments the bioprocessing device 100has two slots 13 into which a cartridge 12 has been inserted into eachslot 13. In general, the bioprocessing devices may have any suitablenumber of slots, such as from about 1 to about 20 slots, such as about 2to about 15 slots, about 3 to about 12 slots, from about 4 to about 10slots, from about 6 to about 8 slots. In some embodiments, only one card12 and one slot 13 may be used during a run. In some embodiments, everyslot 13 may be used with a cartridges 12 during a run. In general, anoperator may use keypad 18 to turn the device on and to interact withthe device, such as a computer control system or central processing unitincluded in the device to select various options and perform variousfunctions or provide and/or respond to commands or queries inconjunction with the graphical user interface (GUI) 15, which mayprovide status information, prompting information, protocol selectioninformation, protocol generation information, protocol storageinformation and any other suitable information to the operator. Inaddition, the GUI may be used to override a protocol before or during arun, if needed. The GUI 15 may be any suitable display device, such asfor example liquid crystal display (LCD) touchscreens, light emittingdiodes (LEDs), or cathode ray tubes (CRTs).

FIG. 1B shows an alternate embodiment of a bioprocessing device 100, asviewed from the front. Bioprocessing device 100 has bioprocessingcartridges 102 inserted into slots 112. As shown in FIG. 1B,bioprocessing device 100 also includes GUI 104, keypad 106, drawer 114having handle 108, each of which may be incorporated into or surroundedby chassis 110.

FIG. 1C shows an alternate embodiment of a bioprocessing device 100including a GUI 104 for displaying information to a user, such asprotocol information or status, run information, protocol details,protocol selection, and other options. In some embodiments, the device100 may be configured with one, two, three, four, or more than fourslots 112, which may all be loaded and/or used at the same time, orsimultaneously. Bioprocessing device 100 may also include a keypad 106on the GUI 104 for inputting and selecting options on the device, and adrawer 114 having handle 108, each of which may be incorporated into orsurrounded by chassis 110. FIG. 1D shows the bioprocessing device 100 ofFIG. 1C as viewed from the front, having a GUI 104 with a keypad 106, adrawer 114, a handle 108, and the surrounding chassis 110.

FIG. 2A shows a rear view of an embodiment of a bioprocessing device 200having cartridges 210 inserted therein. Bioprocessing device 200 hasuniversal service bus (USB) ports 220 which may be used by an operatoror a technician to download information from the device, such as forexample, protocol run information or device service information fromself diagnostic software or firmware that may be installed on the deviceto compatible storage devices. Alternatively, USB ports 220 may be usedto upload software or firmware updates and patches or additionalprotocols onto a computer control system within the device.Bioprocessing device 200 may also include house or auxiliary airconnector 225 for connection of the device to an external air supply,and power connection 230 for connection of the device to a source ofelectrical power such as a DC or AC power source. In some embodiments ofthe devices 200, house air and/or house vacuum may be used rather thanincluding a compressor and a vacuum pump within the device.

A rear perspective view of an alternate embodiment of the device withcartridges 210 inserted into slots 212 is shown in FIG. 2B. The deviceshown in FIG. 2B also shows a power switch 218, power cord slot 235 andutility connections 216, which may be used to supply air, vacuum and/orother utilities to bioprocessing device 200. FIG. 2C shows an alternaterear view of a bioprocessing device 200 with USB ports 216, power cordslot 235, and optional reservoir drain connection 212.

FIG. 3A shows a view of an embodiment of the keypad 310 and GUI 320 ofan embodiment of the bioprocessing device at the protocol selection step330 of the process. As shown, the user may choose to select one ofmultiple protocols preloaded on the system. Any number of preloadedprotocols may be included with the device and displayed on the GUI 320including 1 or more protocols, 2 or more, 3 or more, 5 or more, 10 ormore protocols, or any other suitable number of protocols that can beloaded into the memory of the GUI 320. In some embodiments, a preloadedprotocol may be edited or modified by a user. Additionally, a protocolwith user defined parameters may be entered into the GUI 320. The systemmay also include a time stamp 325. Keypad 310 provides directionalbuttons 335 for navigating in and to different windows on the GUI 320and selection buttons 340 for selecting various options depending on thewindow and commands/functions available.

FIG. 3B shows a view of an embodiment of the keypad 310 and GUI 320 ofan embodiment of the bioprocessing device while a bioprocessing protocolrun is in process. As shown, a Western Breeze protocol 335 has beenselected, a blocking step 337 has been completed and a 30 minute primaryantibody step 338 is in process. Additional steps 341 to be performedmay be displayed with the run times 343 set up for each additional step.Also active on this screen are selection buttons 342 and 344 for pausingor stopping the process respectively. Additional selection buttons 343may be provided, as shown in FIG. 3B, which may be used to changeparameters of a step, advance to the next step before the run time forthe current step has been completed, cancel a step, cancel the run, ormay be used for any other suitable function. The duration time for theentire protocol 350, the number of steps in the protocol 360, and thetime remaining or elapsed 355 on the current step may also be shown onthe screen of the GUI 320. It should be understood that the automatedcontrol system may provide for changing any of the step durations, thesequence of steps, types of steps, number of steps, display options,alarm options and any other suitable parameters for inputting, running,controlling and recording any suitable protocol on the bioprocessingdevice and cartridges inserted therein.

FIG. 4 illustrates a partially exploded view of an embodiment of abioprocessing device 400 and relevant components. The device 400 isshown having two slots 412 with two cartridges 414 ready to bepositioned within the slots 412 of the device. The two cartridges mayinclude at least one, at least two, at least three, or at least fourprocessing chambers 440 for performing various steps of a protocol run.The cartridges 412 may further include sippers 442 that are incommunication, preferably fluid communication, with the fluid reservoirs444 of the device 400. The drawer 418 of the device 400 may include ahandle 416 and is shown in the open position. Drawer slides 456 may beused to facilitate the opening and closing of the drawer 418. In someembodiments, the slides 456 may be located along the bottom of thedrawer, or alternatively, may be located along the sides of the drawer.The drawer may have supports 454 for aligning the fluid reservoir tray446 and waste container 448 in the machine for proper alignment with thesippers 442 on the cartridge 414. The drawer may in some embodimentshouse at least one fluid reservoir tray 446 and waste container 448. Asample container 450 may be inserted into the waste container 448. Thefluid reservoir tray 446 may also be positioned in the waste container448 and may include at least one reagent reservoir 447 for containingand confining at least one reagent. The fluid reservoir tray 446 may befurther configured to hold a collection tube 452 into which the purifiedsample may be collected.

FIG. 5 shows an embodiment of a bioprocessing device 500 with theexternal housing removed. Bioprocessing device 500 may include at leastone vacuum reservoir 505 and/or at least one vacuum pump 510 forsupplying vacuum or suction as needed during processing to thebioprocessing cartridges 515 having aspiration/expiration tubes 517 inslots 520 and cartridge holders 525. Similarly, bioprocessing device 500includes at least one pressure reservoir 530 and/or at least onecompressor 535 for supplying air pressure to the bioprocessingcartridges 515 during processing. In some embodiments, at least one ofthe vacuum reservoir 505, vacuum pump 510, pressure reservoir 550 andcompressor 535 are in fluid communication with the cartridge 515 usingtubing or other suitable vacuum or pressure connectors. In someembodiments, a diffuser may be in communication with the vacuum orpressure connectors to self-adjust the level of pressure/suction beingdelivered to the cartridge. The pressure or vacuum supplied to thecartridge may be controlled according to the configuration of thebioprocessing cartridge or may be a consistent preset pressure (up to 50psi) and vacuum (up to 20 in Hg). In a specific example, the pumpingmechanism of the bioprocessing device has a pneumatic valve responsetime of 20 ms, an air reservoir capacity of 37.7 in³ (both vacuum andpressure), an air compressor pump duty cycle of 50% duty (both vacuumand pressure), and an air compressor pump pressure of 80 PSI.

As shown, removable fluid container tray 540 may be movably engaged withtray slides 545 which may help guide tray 540 as it is moved into andout of bioprocessing device 500. Tray 540 may house fluid containerholder 550, which, in the embodiment shown may comprise waste reservoir555, container receptacle 560 and container retention plate 562. Asshown, containers 565 may be inserted into appropriately sized containerslots 570 on container receptacle 560 and container retention plate 562may be placed atop some or all of the containers 565 to secure thecontainers 565 in place, for example when dumping excess reagents orwaste from the fluid container holder 550. Container receptacle 560 alsoincludes waste reservoir access penetrations 575 which, when alignedwith waste aspiration/expiration tube penetrations 580 on containerretention plate 562, provides access to the waster reservoir 555 toaspiration/expiration tubes on one or more bioprocessing cartridges 515that have been inserted into the device. In some embodiments, the fluidcontainer holder 550 is configured such that aspiration/expiration tubeson one or more bioprocessing cartridges align with the appropriatecontainers or receptacles on the fluid container holder 550 to allow forrunning of a desired bioprocessing protocol. Alternatively, in someembodiments, the fluid container holder 550 is configured such that afluid manifold in the bioprocessing device 500 may access theappropriate containers or receptacles on the fluid container holder 550to allow for running of a desired bioprocessing protocol.

Though shown having a specific configuration, it should be understoodthat the fluid container holder may have any suitable configuration andthat multiple different types, sizes and shapes of containers 565 andconfigurations of container receptacles 560 may be used depending on thefluid types and volumes required for the individual steps of protocolsperformed using the bioprocessing device. For example instead ofcomprising a single integrated fluid container holder that providesslots for housing reagents and samples, multiple individual fluidcontainer holders may be used and placed in the removable fluidcontainer tray or fluid container holders that are sized for all of thefluid containers for a single slot may be used. Similarly, the fluidcontainer holder may be supplied with or without fluid containers andwhen supplied with fluid containers, one or more or all of the fluidcontainers may be supplied empty, sterile, clean, pre-filled and/orendotoxin free. In addition, in some embodiments, the fluid containerholders and some or all of the reagents and the waste containers may besupplied as part of a pre-filled kit, where the user may only need tosupply a sample, where a sample is provided for in the protocol, or oneor more of the reagents as necessary.

Referring to FIG. 6 showing an exploded view of an embodiment of a fluidcontainer holder 600 and removable fluid container drawer 612 and fluidcontainer tray 610, in some embodiments a fluid container holder 600 maycomprise a waste reservoir 615, a container receptacle 617 comprising acontainer holder bottom 620 and a container holder top 625 and havingcontainer slots 630 into which containers 635 may be inserted. Wastereservoir 615 may include a waste level sensor 616 that may providefeedback to an automated control system within a bioprocessing device,which may display a notice on the GUI and/or provide for an audiblealarm. Waste reservoir 615 may also include a fluid drain nozzle thatmay fit through a penetration in the housing of a bioprocessing deviceand may be connected to an appropriate drain or other waste fluidreceptacle. Container receptacle 617 may include waste reservoir accesspenetrations 618 for placing one or more waste lines from abioprocessing cartridge and/or from a fluid manifold in fluidcommunication with the waste reservoir 615. Fluid container holder 600may also include a container retention plate 640. As shown, the fluidcontainer holder 600, when assembled with appropriate containers andreagents and samples as necessary for the desired bioprocessingprotocol, may be placed in to removable fluid container tray 610, whichmay be moved into and out of a bioprocessing device like a drawer.

Referring to FIG. 7 in some embodiments, a fluid container holder 700may be provided that includes a container receptacle 710, which may alsoserve as a waste reservoir, a sample container 715, which may include asample container lid 720, and a reagent reservoir tray 725, which mayinclude multiple reagents reservoirs 730 for containing reagents as partof a pre-filled kit, or may include one or more empty reagent containersor empty reagent receptacles for containing a reagent. In someembodiments, where the all or some of the reagent reservoirs arepre-filled, the reagent tray may be all or partially covered with analuminum, plastic, or any other suitable film, which can then be brokenprior to usage either before the tray is inserted into the device orafter the tray has been positioned in the device. The reagent orreagents may be buffers, including but not limited to, wash buffers,lysis buffers, neutralization buffers, resuspension buffers,precipitation buffers or any other suitable buffer, or other suitablereagents, such as antibodies, standards, blocking solutions, deionizedwater. In some embodiments, the reagent may be ETOH, e.g. 70% ETOH (70%ETOH with 30% NanoPure water, isopropanol, Genomed wash solution,Genomed elution solution, Rnase, or any other suitable reagent, rabbitantibodies, bovine serum albumin (BSA), standards such as MagicMark™standard, and chemiluminescent anti-antibodies, such as Western Breeze®Chemiluminescent kit-Anti-Rabbit. The system may be suitable for usewith all chromogenic, chemiluminescent, and fluorescent immunodetectionreagents and protocols. In some embodiments, the reagents may besupplied as pre-filled reagents in appropriate sized reagent vials andbottles. In some embodiments, the reagents may be added to suppliedreagent bottles and/or vials that are placed in the reagent tray of thedevice. The fluid container lid 720 may include an access penetration toallow for placing of a sample into sample container 715 and forprocessing of the sample on a bioprocessing cartridge. In someembodiments, the fluid container holder 700 is configured such thataspiration/expiration tubes on one or more bioprocessing cartridgesalign with the appropriate containers or receptacles on the fluidcontainer holder 700 to allow for running of a desired bioprocessingprotocol. Alternatively, in some embodiments, the fluid container holder700 is configured such that a fluid manifold in a bioprocessing devicemay access the appropriate containers or receptacles on the fluidcontainer holder 700 to allow for running of a desired bioprocessingprotocol.

FIG. 8A shows an embodiment of a reagent reservoir tray 825. The reagentreservoir tray 825 may have between about 1 and about 15, between about1 and about 10, between about 1 and about 7, between about 1 and about5, between about 1 and about 3 reagent reservoirs 830. In someembodiments, the reagent reservoir tray 825 may include at least 1reagent reservoir, at least 2 reagent reservoirs, at least 5 reagentreservoirs, or at least 12 reagent reservoirs. The shape of the reagentreservoir 830 may be circular, square, polygonal, or any other suitableshape for containing a reagent of suitable volume for containing adesired amount of reagent. In some embodiments, the reagent reservoirtray 825 may further include at least one tube holder 835 into which acollection tube or container for collecting a purified sample can beinserted. The tube holder 835 may either be a hole into which acollection tube may be inserted or may be a structure for receiving andsupporting a collection tuber inserted therein. In some embodiments, thereagent reservoir tray may comprise more than one tube holder. In someembodiments, the tube holder 835 may be configured to hold a collectiontube with a volume of about 100 uL, about 1 mL, about 2 mL, about 5 mL,or about 10 mL tube. The reagent reservoirs 830 may further comprise atleast one sipper 840 in the reagent reservoir which is in preferablyfluid communication with a portion of the bioprocessing cartridge. Thesippers 840 may be configured in any suitable configuration for allowingthe reagent in the reagent reservoir to collect in the sipper 840 andthereby allowing a substantial part of the reagent to be in introducedinto a bioprocessing cartridge and at the same time reducing bubblesfrom entering the bioprocessing cartridge. In some embodiments, thereagent reservoir tray 825 may include an opening 831 to provide fluidcommunication to a waste tray

A perspective view of an alternate embodiment of a reagent reservoirtray 825 with alternate embodiments/configurations of reagent reservoirs830 is shown in FIG. 8B. In some embodiments, the reagent reservoir tray825 may include posts 827 for supporting and/or positioning the reagentreservoir tray 825 in the drawer and/or waste tray. The reagentreservoir tray 825 may include at least one reagent reservoir 830 forcontaining and confining a reagent, at least one tube holder 835, and atleast one opening 831 to waste, as shown in FIG. 8C. In someembodiments, at least one reagent reservoir 830 may further include asipper 840 configured to facilitate the movement of reagent between thebioprocessing cartridge and the individual reagent reservoirs 830 of thereagent reservoir tray 825. FIG. 8D is a side view of the reagentreservoir tray 825 showing the reagent reservoirs 830, the tube holder835, and sippers 840. The reagent reservoirs 830 may be substantiallythe same depth with respect to each other or they may vary with respectto each other. In some embodiments, the depth of the individual reagentreservoirs 830 may depend on the length of the aspiration/expirationtubes of the cartridge. FIG. 8E is a cross-sectional view of a reagentreservoir tray 825 showing the tube holder 835, the reagent reservoirs830 and the sippers 840 located at the bottom of each reservoir 830.FIG. 8F is a close-up view of the sippers 845 located in the bottom oftwo different reagent containers 830. FIG. 8G illustrates an embodimentof a reagent reservoir tray as viewed from the bottom of the tray, thesippers 840 extending from the bottom of each reagent reservoir 830, andthe opening 831 to waste. The reagent reservoir tray can be configuredto hold a suitable number and/or amount of reagents, for examplepurposes only, the reagent reservoir tray 825 may include at least of aone collection tube slot or tube holder, a TE buffer reservoir, and 70%Ethanol reservoir, an isopropyl reservoir, an elution buffer reservoir,a resuspension buffer reservoir, and a wash buffer reservoir.

FIGS. 9A and 9B show opposite side perspective views of an embodiment ofa cartridge holder 900 with a bioprocessing cartridge 905 insertedtherein. As shown, cartridge holder 900 includes spring loaded housingbolts 910 which provide for connection of opposing holder sides 915 and920 via interaction with support plates 925 and 930. Support plate 930may include individual supply connectors 932 (as shown in FIG. 9B) aspart of a manifold for supplying control fluids to a bioprocessingcartridge. The individual supply connectors 932 may provide connectionof a control fluid manifold to control fluid connectors on bioprocessingcartridge 905. Cartridge holder 900 may also include an inflatablebladder or sack 945, which may be connected to a pressure source via abladder inflation/deflation line 950. Cartridge holder 900 may alsoinclude attachment slots 955 that may provide for attachment of holder900 in a slot of a bioprocessing device.

FIGS. 10A and 10B show side views of a cartridge holder 1000 of abioprocessing device. As shown, cartridge holder 1000 includes springloaded housing bolts 1010 which include spring 1012 for urging supportplate 1030 apart from support plate 1025, while urging opposing holdersides 1015 and 1020 together. Also shown in FIG. 10A is inflatablebladder or sack 1045 in a deflated state. Upon inflation of the bladder1045, cartridge holder appears as shown in FIG. 10B, showing inflatedbladder 1050 urging the two opposing holder sides 1015 and 1020 as aunit towards support plate 1030, thereby compressing spring 1012. Inthis manner, by holding support plate 1025 stationary, the opposingholder sides 1015 and 1020 housing and a bioprocessing cartridge heldtherein may be moved towards support plate 1030. In this manner (and asshown in better detail in FIGS. 11A and 11B), the control fluidconnectors of a bioprocessing cartridge may be urged into fluidcommunication with supply connectors on support plate 1030 and thesupply connectors may be connected to the control fluid manifold. Insome embodiments, pressure and vacuum may be provided to thebioprocessing cartridges to control the opening and closing of valvesand to control the actuation of pumps, thereby controlling the flow offluids throughout the channels in a bioprocessing cartridge. It shouldbe understood that other mechanisms of achieving the connection betweenthe control fluid connectors and the supply connectors may be usedinclude manual latches, locking latches, mechanical or electricallydriven connections and the like.

FIGS. 11A and 11B show cross-sectional views of an embodiment of thecartridge holder 1000 shown in FIGS. 10A and 10B. As shown in FIGS. 11Aand 11B, when bladder 1145 is in a deflated state as shown in FIG. 11A,control fluid connectors 1160 on bioprocessing cartridge 1105 are notengaged with supply connectors 1132 on support plate 1130. Uponinflation of bladder 1145 to form inflated bladder 1150, the opposingholder sides 1115 and 1120 and bioprocessing cartridge 1105 held thereinare moved towards support plate 1130 and supply connectors 1132,compressing gasket 1170 and forming a seal 1175 between the supplyconnectors 1132, the gasket 1170 and the control fluid connectors 1160and placing the supply connectors 1132 in fluid communication withcontrol fluid connectors 1160.

FIG. 12 shows an exploded view of an embodiment of a bioprocessingcartridge 1200.

Cartridge 1200 has two film or foil layers 1202 and 1204 which may besealed, such as heat sealed onto the exterior face of the process fluidlayer 1206 and the exterior face of the control layer 1208 of thecartridge 1200. The film layers 1202, 1204 may comprise any suitableplastic film, such as coated plastic film, or suitable metallic film,such as metallic foils or coated metallic foils, including aluminumfoils, and the films may be coated with any appropriate coating and/oradhesives, such as heat seal adhesive. In some embodiments, the film maybe a PET film with a PE tie layer that is coated with a heat sealadhesive on the face that is in contact with the process fluid layer1206 or control layer 1208. In other embodiments, the film layers maycomprise aluminum foil that is coated with a heat seal adhesive on theface that is in contact with the process fluid layer 1206 or controllayer 1208. The film layers may include penetrations 1210 for thecontrol fluid connectors, penetrations 1212 for alignment guides 1214for aligning the process fluid layer 1206 and the control layer 1208. Insome embodiment, the card may include a penetration to provide viewingaccess to a color indicator chamber. When sealed onto the relevantsurface of the cartridge 1200, the film layers 1202 and 1204 may formthe final wall for the process fluid channels 1220 on fluid layer 1206and the control fluid channels 1240 on control layer 1208.

The cartridge 1200 may include a process fluid layer 1206 havingmultiple process fluid channels 1220 and multiple penetrations 1222through which control fluid connectors may be placed, and multiplepenetrations 1224 for alignment guides. Process fluid channels 1220 mayspan the entire process fluid layer 1206. Alternatively, the processfluid channels may be open on the front or exterior surface of the layerand not open on the back or interior surface of the layer. In thismanner, process fluid channels 1220 may be isolated from the controlfluid layer 1208, except where layer pass-throughs or pass-throughvalves are provided and when applied to the process fluid layer 1206,film layer 1202 may complete the walls of the process fluid channels1220. In addition, process fluid layer 1206 may include access valvecompartments 1226, process valve compartments 1227, pump compartment228, bioprocessing compartment 1230 having support ribs 1231, colorindicator compartment 1232, check valve compartment 1233, process fluidconnectors 1234 and gripper 1236.

Cartridge 1200 may also include control fluid layer 1208 having controlfluid channels 1240 and control fluid connectors 1242. Control fluidchannels 1240 may span the entire control fluid layer 1208 oralternatively, may instead be open on the back or exterior surface ofthe layer and not open on the front or interior surface of the layer. Inthis manner, control fluid channels 1240 may be isolated from theprocess fluid layer 1206, except where layer pass-throughs orpass-through valves are provided and, in some embodiments, when appliedto the control fluid layer 1208, a film layer 1204 may complete thewalls of the control fluid channels 1240. In addition, control fluidlayer may include at least one of access valve compartments 1246,process valve compartments 1247, pump compartment 1248, bioprocessingcompartment 1250, color indicator compartment 1252, check valvecompartment 1253 and gripper 1256.

Cartridge 1200 may also include access valve membranes 1260, processvalve membranes 1261, pump membrane 1262, and gaskets 1264 between theinterior faces of the process fluid layer 1206 and the control fluidlayer 1208. In some embodiments, the cartridge 1200 may include at leastone check valve membrane 1263. In the embodiment shown,aspiration/expiration tubes 1266 are also included as part of cartridge1200. When assembled, access valve membranes 1260 fit into compartmentsformed by the access valve compartments 1226 and 1246 on the processfluid layer 1206 and control fluid layer 1208 to form the access valvessealed by pinching the membranes between the two layers. Fluid may flowinto the valves via process fluid channels 1220 connected to the processfluid side of the valve membranes and the valves may be opened or closedusing pressure or vacuum supplied using the control fluid channels 1240on the control fluid side of the valve membranes. In this manner,process valves may be formed by fitting the process valve membranes 1261into compartments formed by the process valve compartments 1227 and1247, the pump may be formed by fitting the pump membrane 1262 into thepump compartments 1228 and 1248, the bioprocessing chamber may be formedby aligning the bioprocessing compartments 1230 and 1250, the colorindicator chamber may be formed by aligning the color indicatorcompartments 1232 and 1252, the check valve, if present, may be formedby fitting the check valve membrane 1263 into the check valvecompartments 1233 and 1253 and the control fluid connectors 1242 may beprovided with sealing gaskets by placing the gaskets over the controlfluid connectors 1242 and allowing the smaller opening of the controlfluid connector penetrations 1222 on the process fluid layer 1206 tohold the gasket in place. As shown, in this embodiment, thebioprocessing chamber formed by the bioprocessing compartments 1230 and1250 may be open at the top for access by a user. In addition, the films1202 and 1204 may be sealed to the exterior surfaces of the processfluid layer 1206 and control layer 1208 sealing the fluid channels 1220and 1240 and forming one wall for the channels.

When assembled, the bioprocessing cartridge of FIG. 13 may appear asshown, with front and back views respectfully in FIGS. 13A and 13B. Asshown, the visible portions of the cartridge 1300 when assembled mayinclude grippers 1305, bioprocessing chamber 1310 with support ribs1312, film layers 1315 and 1320, color indicator chamber 1325, processfluid connectors 1327, control fluid connectors 1330,aspiration/expiration tubes 1335 and slot alignment guide 1340.

In addition, a transparent view of the assembled bioprocessing cartridgeof FIG. 13 is shown in FIG. 14. As shown, bioprocessing cartridge 1400is viewed through film layer 1405 on the surface of the process fluidlayer and the view extends through each of the layers from the front.FIG. 14 shows process fluid channels 1410 on the process fluid layer,access valves 1415, control fluid connectors 1420, check valve 1430,color indicator chamber 1435, process valves 1440, pump 1445, alignmentguides 1450, slot alignment guide 1455, bioprocessing chamber 1460 withsupport ribs 1462, gripper 1465, control fluid channels 1470 on thecontrol fluid layer and aspiration/expiration tubes 1475.

FIG. 15 shows a detail view of an embodiment of the connection 1500between an aspiration/expiration tube 1505 and a process fluid connector1510 on a bioprocessing cartridge 1515. As shown, process fluidconnector 1510 may be provided with one or more retention rings 1520which may provide a clearance fit with a corresponding retention groove1525 on the inner wall of the aspiration/expiration tube 1505. Processfluid connector 1510 includes one or more sealing grooves 1530, whichmay provide an interference fit with sealing rings 1535 on the innerwall of aspiration/expiration tube 1505. In this manner, retention rings1520 may secure the aspiration/expiration tube 1505 to the process fluidconnector 1510, while the sealing rings 1535 may provide for sealing ofthe aspiration/expiration tube 1505 to the process fluid connector 1510.It should be understood that many alternative connections may be used toprovide aspiration/expiration tubes connected to the cartridges and thatthe tubes may also be formed integrally with the cartridges.

FIG. 16A shows an exploded view of an embodiment of a bioprocessingcartridge 1600. Cartridge 1600 has two film or foil layers 1602 and 1604which may be sealed, such as heat sealed or adhesive sealed onto theexterior face of the process fluid layer 1606 and the exterior face ofthe control or pneumatic layer 1608 of the cartridge 1600. The filmlayers 1602, 1604 may include any suitable plastic film, such as coatedplastic films, or suitable metallic film, such as metallic foils orcoated metallic foils, including aluminum foils, and the films may becoated with any appropriate coating and/or adhesives, such as heat sealadhesive. In some embodiments, the film may be a PET film with a PE tielayer that is coated with a heat seal adhesive on the face that is incontact with the process fluid layer 1606 or pneumatic layer 1608. Inother embodiments, the film layers may comprise aluminum foil that iscoated with a heat seal adhesive on the face that is in contact with theprocess fluid layer 1606 or pneumatic layer 1608. The film layers mayinclude penetrations 1603 for the control fluid connectors 1642,penetrations 1605 for alignment guides 1611 and, in some embodiments, apenetration to provide viewing access to a color indicator chamber, ifpresent. When sealed onto the relevant surface of the cartridge 1600,the film layers 1602 and 1604 may form the final wall for the processfluid channels 1620 on fluid layer 1606 and the pneumatic channels 1640on pneumatic layer 1608.

The cartridge 1600 may include a process fluid layer 1606 havingmultiple process fluid channels 1620. Process fluid channels 1620 mayspan the entire process fluid layer 1606 or alternatively, may be openon the front or exterior surface of the layer and not open on the backor interior surface of the layer. In this manner, process fluid channels1620 may be isolated from the control fluid layer 1608, except wherelayer pass-throughs or pass-through valves are provided and when appliedto the process fluid layer 1606, film layer 1602 may complete the wallsof the process fluid channels 1620.

Cartridge 1600 may also include pneumatic layer 1608 having pneumaticchannels 1640 and pneumatic connectors 1642. Pneumatic channels 1640 mayspan the entire pneumatic layer 1608 or, alternatively, may instead beopen on the back or exterior surface of the layer and not open on thefront or interior surface of the layer. In this manner, pneumaticchannels 1640 may be isolated from the process fluid layer 1606, exceptwhere layer pass-throughs or pass-through valves are provided and whenapplied to the pneumatic layer 1608, film layer 1604 may complete thewalls of the pneumatic channels 1640.

As shown, each of the pneumatic or control layer 1608 and the processfluid layer 1606 includes bioprocessing chamber compartments 1603, 1605,1607 and 1609, pump compartments 1610 and valves 1654, and access valvecompartments 1618 and valves 1650, process valve compartments 1644 andvalves 1652, and in some embodiments, check valve compartments 1646 andvalves 1656. In some embodiments, the cartridge 1600 may includepass-through penetrations 1673. The control layer 1608 may also includescontrol fluid connectors 1642, which may include with gaskets.

In some embodiments, a bioprocessing chamber may include a filter 1662,1664, 1666, and 1668, O-rings 1684, and gaskets 1685, 1687 as is shownin the exploded view of bioprocessing cartridge 1600. In someembodiments, the filter may be a Bla065 membrane, nitrocellulosemembrane, glass fiber membrane, Xthick membrane, PPTR membrane, AnionExchange membrane or any other suitable filter. In some embodiments, thefilter of a bioprocessing chamber may be supported by a solid support orfrit 1686, 1688. The filter may be a single layer filter or a multiplelayer filter, and may be supported by one or more than one solidsupport, for example as is shown in bioprocessing chamber 1607. The twolayers of the cartridge and the components found in between may besealably joined, such as by ultrasonic or other welding or using anadhesive, latches, clasps, or any other mechanism for joining the twoplastic layers to form an embodiment of a bioprocessing cartridge. Insome embodiments one or more of the bioprocessing compartments includesone or more O-rings and/or tongue and groove components to assist withsealing. In addition, in some embodiments one or more of thebioprocessing chamber compartments on one or both of control layer 1608and the process fluid layer 1606 includes structures, such asprotrusions, along or on one or both of their interior walls to preventor limit interaction of the filter or solid support with the walls ofthe bioprocessing chambers. In some embodiments, rivets 1692 may be usedto further support the membrane and to seal a bioprocessing chamber.

FIG. 16B is a close up view of control fluid connectors 1642 located onthe pneumatic layer 1608. In some embodiments, the control fluidconnectors 1642 further include supports 1693 which provide additionalsupport to the control fluid connectors during attachment of supplytubes to the card. FIG. 16C is a lateral cross-sectional view of onehalf of bioprocessing chamber 1603 showing a gasket 1685, O-rings 1684,1686 and rivets 1692, 1694. FIG. 16D shows a side view of the pneumaticlayer 1608 and the fluid layer 1606, the filter 1683, O-ring 1684, and arivet 1692 creating additional support and/or connecting the pneumaticlayer 1608 and the fluid layer 1606 together.

FIGS. 17A and 17B show views of the interior sides of a control layer1701 and a process fluid layer 1702 of an embodiment of a bioprocessingcartridge 1700. As shown, each of the control layer 1701 of FIG. 17A andthe process fluid layer 1702 of FIG. 17B includes bioprocessing chambercompartments 1703, 1704, 1706 and 1708, pump compartments 1710, 1712,1714 and 1716, access valve compartments 1718, 1720, 1722, 1724, 1726,1728, 1730, 1732, 1734, 1736, 1738, and 1739, process valve compartments1740, 1742, 1744, 1746, 1748, 1750, 1752, 1754, 1756, 1758, 1760 and1762, check valve compartments 1764, 1766, 1768, pass-through checkvalve compartments 1770 and pass-throughs penetrations 1772, 1773, and1774. The control layer 1701 may also include control fluid connectors1776, control fluid channels 1794 and slot alignment guide 1796. Theprocess fluid layer 1702 also includes control fluid connectorpenetrations 1777, process fluid connectors 1778, 1779, 1780, 1781,1782, 1783, 1784, 1785, 1786, 1787, 1788 and 1789 and process fluidchannels 1792.

The control layer 1701 and/or process fluid layer 1702 may have pumpmembranes, valve membranes, O-rings, and solid supports placed withinthe relevant compartments and then the two layers may be sealablyjoined, such as by ultrasonic or other welding or using an adhesive,latches, clasps, clamps, or any other mechanism for joining the twoplastic layers to form an embodiment of a bioprocessing cartridge. Insome embodiments one or more of the bioprocessing compartments includesone or more O-rings and/or tongue and groove components to assist withsealing. In some embodiments, each of bioprocessing chamber compartments1703, 1704, and 1708 include O-rings. In addition, in some embodimentsone or more of the bioprocessing chamber compartments on one or both ofcontrol layer 1701 and the process fluid layer 1702 includes structures,such as protrusions, along or on one or both of their interior walls toprevent or limit interaction of the filter or solid support with thewalls of the bioprocessing chambers.

FIGS. 18A and 18B show front and rear views 1801 and 1802 respectivelyof an embodiment of an assembled bioprocessing cartridge. As shown, thebioprocessing cartridge includes bioprocessing chambers 1803, 1804, 1806and 1808, pumps 1810, 1812, 1814 and 1816, access valves 1818, 1820,1822, 1824, 1826, 1828, 1830, 1832, 1834, 1836, 1838, and 1839, processvalves 1840, 1842, 1844, 1846, 1848, 1850, 1852, 1854, 1856, 1858, 1860and 1862, check valves 1864, 1866, 1868, pass-through check valve 1870,pass-throughs 1872, 1873 and 1874, control fluid connectors 1876,process fluid connectors 1878, 1879, 1880, 1881, 1882, 1883, 1884, 1885,1886, 1887, 1888 and 1889, control fluid gaskets 1890 and 1891, processfluid channels 1892, control fluid channels 1894 and slot alignmentguide 1896.

Each of bioprocessing chambers 1803, 1804, 1806 and 1808 may include asolid support. In some embodiments, where the bioprocessing cartridge isused for purification and collection of nucleic acids, such as DNAincluding plasmids or plasmid DNA from whole cells, bioprocessingchamber 1803 may include a cell separation filter for separating thewhole cells from the cell culture media, bioprocessing chamber 1804 mayinclude a cell lysate clarification filter for clarifying the lysate byfiltering out cellular and other debris within the lysate, bioprocessingchamber 1806 may include a solid phase extraction disk, cassette orfilter to reversibly bind the nucleic acids from the cellular lysate,and bioprocessing chamber 1808 may include a precipitation filter tocapture the DNA eluted from the solid phase extraction disk, cassette orfilter. In some embodiments one or more of the bioprocessing chambersincludes one or more O-rings and or tongue and groove seals. In someembodiments, each of bioprocessing chambers 1803, 1804 and 1808 mayinclude O-rings or gaskets. In addition, in some embodiments one or moreof the bioprocessing chambers includes structures, such as protrusions,along or on one or both of their interior walls to prevent or limitinteraction of the filter or solid support with the walls of thebioprocessing chambers.

Each of access valves 1818-1839, process valves 1840-1862 and checkvalves 1864-1868 may have pinched membranes inside joined compartmentsas described elsewhere herein relative to other bioprocessingcartridges, the process fluid channels 1892 and control fluid channels1894 may be fluid channels as described elsewhere herein with respect tosuch channels and the process fluid connectors 1878-1889 may be processfluid connectors as described elsewhere herein. Control fluid connectors1876 may be as described elsewhere herein, with the exception that, insome embodiments, a single control fluid gasket 1890 and/or 1891 isprovided over a plurality of control fluid connectors and the controlfluid gaskets 1890 and 1891 may be provided externally to thebioprocessing cartridge rather than internally. Pass-through check valve1870 may provide for actively controlled fluid flow between a processfluid layer and a control fluid layer on bioprocessing cartridge 1800,by allowing for flow in only one direction between the layers. In someembodiments, pass-through check valve 1870 may provide for flow from theprocess fluid layer to the control fluid layer, while in otherembodiments, pass-through check valve 1870 may provide for flow from thecontrol fluid layer to the process fluid layer of bioprocessingcartridge 1800. The pass-throughs may provide for fluid communicationbetween a process fluid layer and a control fluid layer on bioprocessingcartridge 1800 in both directions.

The process fluid layers and control fluid layers and theaspiration/expiration tubes of the bioprocessing cartridges may be madefrom any suitable material, such as plastic, such as ABS, polystyrene,polypropylene, polycarbonate and the like and may be injection molded orotherwise formed such as by etching. In some embodiments, thebioprocessing cartridges may be injection molded and may have mesoscalefluid channels. In other embodiments, the bioprocessing cartridges mayhave microscale channels. The valve and pump membranes may be made fromthe same or different materials and may be made from any materialflexible enough to withstand the application of the pressure and vacuumduring the bioprocessing. Examples of some suitable materials includethermoplastics and thermoplastic elastomers, such as SANTOPRENE™, andsilicone. In addition, the membranes may be made from traditionallyrigid materials when the membranes are suitably thin to be flexible,despite the relative general rigidity of the material.

In some embodiments, one or more of the interior surfaces of thebioprocessing chamber may include projections or may be frosted orotherwise surface modified to limit or prevent undesirable interactionbetween a solid support within the chamber and one or more of theinterior surfaces. In addition, when assembling the cartridges,additional sealing surfaces or components may be provided either on thelayers or between the layers to assist in sealing individual portions ofthe cartridges or the periphery of the cartridges. For example, in someembodiments, the bioprocessing cartridges may include one or more O-ringseals and/or tongue in groove or other sealing mechanisms may beincluded in the layers around all or a portion of the periphery of thecartridge, of one or more bioprocessing chambers or of one or morevalves or pumps. Additional sealing of the layers of the cartridges maybe accomplished by sealing the layers together with an adhesive, or byusing ultrasonic or solvent welds or other suitable mechanism forsealing the layers together. In addition, though the bioprocessingcartridges described herein have been described as having two layers, itshould be understood that the bioprocessing cartridges may have anysuitable number of layers depending on the bioprocessing protocol used.For example, bioprocessing cartridges may include multiple process fluidlayers, multiple control fluid layers, or temperature control layersthrough which the temperature of a portion of or through which all ofthe cartridge is controlled. Moreover, instead of providing individualmembranes for the pumps and valves, in some embodiments a singlemembrane layer may be provided that extends across each of the variouscompartments, thereby providing individual membranes for thecompartments as a single layer in the cartridges.

FIGS. 19A and 19B show alternate embodiments of a bioprocessingcartridge. In some embodiments, the bioprocessing cartridge may includeat least one bioprocessing chambers which may include filter covers forthe bioprocessing chamber. For example purposes only, as shown in FIG.19A, at least some of the bioprocessing chambers, 1903 and 1904, mayfurther include filter covers 1905, 1906, respectively. In someembodiments, all the bioprocessing chambers 1903, 1904, 1907, 1908 mayinclude filter covers. In some embodiments, at least one, or at leasttwo, at least three, or more than three bioprocessing chambers includefilter covers. A filter or membrane may be positioned in the fluidicside 1901 of the bioprocessing cartridge, as shown in FIG. 19A and mayserve to seal the bioprocessing chamber. In some embodiments, the filtermay be positioned on the pneumatic side of the card and the filtercovers positioned over the individual bioprocessing chambers. Thepneumatic side 1901 and the fluidic side 1902, may then be aligned andassembled together, as shown in FIG. 19B. The fluidic side 1902 and thepneumatic side 1901 may then be assembled together by any suitablemechanism.

In some embodiments, at least one of the bioprocessing chambers may bemodular as shown in FIGS. 20A & 20B. FIG. 20A shows a bioprocessingcartridge 2000 in which two bioprocessing chambers 2003 and 2004 may beattached to the body 2001 of the cartridge 2000. In some embodiments ofthe bioprocessing cartridge, at least one bioprocessing chamber ismodular and may be attached to the bioprocessing cartridge. FIG. 20Ashows a bioprocessing cartridge 2000 with a modular bioprocessingchamber 2003 including a cell separation filter and a modularbioprocessing chamber 2004 including a cell lysate clarification filter.In some embodiments, the bioprocessing chambers 2003, 20204 may belocated on opposite sides of the bioprocessing cartridge 2000, such asfor example purposes, on opposite sides of the solid phase extractiondisk 2006, as shown in FIG. 20A. In some embodiments, the modularbioprocessing chambers 2003, 2004 may be connected to bioprocessingcartridge 2000 such that the two modular bioprocessing chambers 2003,2004 are connected to each other in series, so that a first modularbioprocessing chamber is attached to the body of the cartridge and thena second modular bioprocessing chamber is attached to the first modularbioprocessing chamber. In some embodiments, at least one, at least two,at least three, or more than three of the components of the cartridgemay be modular. The modular components may include connectors 2011,2013, 2015, and 2117, for example, the male end connectors as shown inFIG. 20A that interface with connectors located on the body 2001 of thecartridge. FIG. 20B shows a close up view of one bioprocessing chamber2003 connected to the bioprocessing card. FIG. 20B shows a bioprocessingchamber 2003 connected to the body 2001 of the cartridge. As shown inFIG. 20B, in some embodiments, the bioprocessing chamber 2003 mayinclude male connectors 2011, 2013 of the modular bioprocessing chamber2003 which interact with female connectors 2019, 2021 located on thebody 2001 of the bioprocessing cartridge. In some embodiments, the maleconnectors are located on the body of the bioprocessing cartridge andthe female connectors are located on bioprocessing chamber module.

FIGS. 21A and 21B show detail views of membrane holders, such as blotmembrane holders, that may be inserted into some embodiments of thebioprocessing cartridges. As shown in FIG. 21A, membrane holder 2100 maycomprise a hinge 2110 connecting the halves 2112 and 2114 of themembrane holder 2100, allowing the halves 2112 and 2114 to be opened orclosed so that a membrane 2116 may be inserted into the holder. Thehalves 2112 and 2114 may include ribs, for example, diagonal ribs 2118to support the structure of the holder while allowing for free flow ofprocess fluids around both sides of the membrane 2116 and preventing orlimiting interaction between the membrane 2116 and the walls of abioprocessing chamber on a bioprocessing cartridge. FIG. 21B shows analternative membrane holder 2120. In some embodiments instead of a hingethe holder may be folded along fold 2122 to form the two portions 2121and 2123 of the holder. Membrane holder 2120 includes fluid flow cutouts2124 to provide non-interfering access to a membrane in the holder 2120from flow channels on a bioprocessing cartridge. Membrane holder 2120may include support ribs 2128, oriented for example in a verticalorientation to provide support to the holder while allowing for freeflow of process fluids around both sides of the membrane and whilelimiting or preventing interaction between the walls of a bioprocessingchamber with a membrane within the holder 2120. The membrane holders maybe constructed from any suitable materials including plastics, such asfor example PVC, HDPE, polyesters, and APET, and may be injection moldedor be assembled from injection molded pieces or may be die cut. In someembodiments, the membrane holders help provide for laminar flow ofprocess fluids across both sides of a membrane in a bioprocessingchamber and prevent the membrane from sticking or contacting one or morewalls of the bioprocessing chamber.

FIG. 22A shows an alternative embodiment of a blot membrane holder 2200that is similar to the blot membrane holder 2120 shown in FIG. 21B. Blotmembrane holder 2200 is folded similar to the blot membrane holder 2120in that holder 2200 is folded along fold 2222 to form two portions,portion 2221 and portion 2223, of holder 2200 between which a blotmembrane may be placed. Unlike holder 2120, holder 2200 includes bottomfluid flow cutouts 2227 along fold 2222 to facilitate fluid flow arounda blot membrane in the holder 2200 and between the bioprocessing chamberand the fluid flow channels on a bioprocessing cartridge in addition tothe side fluid flow cutouts 2224. Similar to blot membrane holder 2120,holder 2200 includes support ribs 2228 shown in a vertical orientationin the figure to provide support to the holder while allowing for freeflow of process fluids around both sides of the membrane and whilelimiting or preventing interaction between the walls of a bioprocessingchamber with a membrane within the holder 2200. Blot membrane holder2200 may be constructed from the same or similar materials from whichthe other blot membrane holders described herein are constructed.

FIG. 22B shows an alternative embodiment of a blot membrane holder 2250that is similar to the blot membrane holder 2200 shown in FIG. 22A. Blotmembrane holder 2250 is folded similar to the blot membrane holder 2200in that holder 2250 is folded along fold 2252 to form two portions, afirst portion 2251 and a second portion 2253, of holder 2250 betweenwhich a blot membrane may be placed. In addition, like holder 2200,holder 2250 includes bottom fluid flow cutouts 2257 along fold 2252 tofacilitate fluid flow around a blot membrane in the holder 2250 andbetween the bioprocessing chamber and the fluid flow channels on abioprocessing cartridge in addition to the side fluid flow cutouts 2254.Unlike holder 2200, blot membrane holder 2250 includes side fluid flowcutouts only on portion 2251 and not on portion 2253 and blot membraneholder 2250 also includes bumps or nibs 2260 that facilitate separationof the two portions 2251 and 2253 and provide a more consistent area forprocessing a blot membrane. Similar to blot membrane holder 2200, holder2250 includes support ribs 2258 shown in a vertical orientation in thefigure to provide support to the holder while allowing for free flow ofprocess fluids around both sides of the membrane and while limiting orpreventing interaction between the walls of a bioprocessing chamber witha membrane within the holder 2250. Blot membrane holder 2250 may beconstructed from the same or similar materials from which the other blotmembrane holders described herein are constructed.

FIG. 23 shows a basic flowchart 2300 of one embodiment of a method forperforming some of the steps that may be included in performingbioprocessing protocols using the automated control system on someembodiments of the bioprocessing device provided herein. These steps areintended to be by way of example only, and some embodiments may includeadditional steps, different orders of steps and may omit some of thesteps shown. As shown, the device may be initialized 2310, the typeand/or number of cartridges inserted into the cartridge slots of thedevice may be identified 2320 and a bioprocessing protocol may beselected 2330 either from an available set of pre-loaded protocols ormay be user generated on the device either by editing a pre-existingprotocol or by entering a new protocol onto the device or by uploading aprotocol onto the device. After selection of the protocol 2330, thedevice may prompt the user to confirm acceptance and correctness of theindividual parameters associated with a protocol 2335 and then theprotocol may be executed 2340 by the device on the desired cartridges.In some embodiments, multiple protocols, multiple types of protocolsand/or multiple types of cartridges may be used at the same time or invarious sequences on the device.

By way of example, embodiments of the bioprocessing cartridge asdisclosed with respect FIGS. 12-14 may be used in conjunction with abioprocessing device described herein to perform any or all of theblocking, washing, antibody binding, and/or detection steps of a westernblot after the protein is transferred to the blot membrane. An exampleof one embodiment of how such a process may be conducted follows. Itshould be understood that the following procedure is provided by way ofexample only and that one or more of the steps may be modified and/ordeleted and that other types of bioprocessing may be performed using thebioprocessing device and bioprocessing cartridge and other protocols andthe same or different bioprocessing cartridge configurations:

1) A bioprocessing device is prepared for processing by inserting afluid container holder into the removable fluid holder tray and slidinto the bioprocessing device. The fluid container holder includes, foreach blot membrane to be processed, a container containing anappropriate amount of blocking buffer, a container containing anappropriate amount of wash buffer, a container containing an appropriateamount of primary antibody, a container containing an appropriate amountof secondary antibody and a container containing an appropriate amountof water. It should be understood that the fluid container holder may besupplied to the user with one or more of the containers, that may besupplied pre-filled or may be filled by the user. In some embodiments,at least one or the containers is pre-filled, while in other embodimentsall or none of the containers are pre-filled.

2) A blot membrane upon which the protein to be detected has beentransferred is inserted into a blot membrane holder and into thebioprocessing chamber of a bioprocessing cartridge configured asdescribed in FIGS. 12-14 through the open top of the bioprocessingchamber. Multiple cartridges may be used, each with its own blotmembrane, blot membrane holder and fluid containers in the fluidcontainer holder.

3) The bioprocessing cartridges are inserted into the slots of thebioprocessing device and secured to the cartridge holders. The fluidmanifolds for each cartridge are attached to the control fluidconnectors of the cartridge by inflating the bladders associated witheach cartridge holder. The operator ensures that theaspiration/expiration tubes are placed within the appropriate containerson the fluid container holder.

4) The bioprocessing device may confirm proper insertion of the tray andthe cartridges and that the cartridges have not been used previously.

5) The operator selects a desired protocol on the automated controlsystem for the cartridges and initiates it. All of the access valves areensured to be closed at this time by verifying their actuation state.

The remainder of this example procedure will be described with respectto a single cartridge and occurs automatically and hands-free once theprotocol is selected:

6) The automated control system, using pressure and/or vacuum throughthe appropriate control fluid channels actuates the membrane of theaccess valve associated with the blocking buffer container to open andactuates the pump and the process fluid valve associated with flowchannel connecting to the lower center portion of the bioprocessingchamber (the “center valve”) on the cartridge to pump blocking bufferfrom the blocking buffer container and into the bioprocessing chamber.After the blocking buffer has been pumped into the bioprocessingchamber, the blocking buffer access valve is actuated to a closedposition.

7) Blocking buffer is recirculated across the bioprocessing chamber andthe blot membrane by withdrawing buffer through one of the process fluidvalves associated with the flow channels entering the side of thebioprocessing chamber (“the side valve”) by actuating the pump and thenpumping the withdrawn fluid back into the bioprocessing chamber throughthe center valve. Either side valve may be used depending on the size ofthe blot membrane. The recirculation may occur as follows. The sidevalve is opened and buffer is pumped into the pump through the sidevalve and the associated flow channel. The side valve is closed and thecenter valve is opened. The pump is actuated to pump the blocking bufferfrom the pump into the bioprocessing chamber through the center valveand the center valve is closed and the procedure is repeated for theselected time in the protocol. Each return of fluid to the bioprocessingchamber may cause the blot membrane to move slightly and may causelocalized formation of eddies or formation of turbulence that ensuresgood or substantially uniform exposure of the surface of the blotmembrane to the blocking buffer.

8) Once blocking is complete, the buffer is pumped from the chamberthrough the center valve and into a waste container on the fluidcontainer holder by alternately opening the center valve, pumping fluidinto the pump, closing the center valve, opening the waste containeraccess valve and pumping the fluid into the waste container.

9) In this manner, the blot membrane may be washed, primary antibody maybe incubated with the membrane, the membrane may be washed again,secondary antibody may be incubated with the membrane, the membranemaybe further washed and rinsed all according to the automated protocolwith no interaction with the user required. Any or all of the abovesteps may include recirculation of the process fluid described above.After the final rinse, the device may provide an alarm to signalcompletion and the cartridges may be removed from the device and theblot membranes removed from the cartridges for further processing, suchas protein detection and analysis.

The antibodies, blocking buffers, wash buffers, anddevelopment/detection solutions may include any suitable compositionsfor use in immunoblotting procedures without limitation. The antibodies,blocking buffers and wash buffers may be supplied commercially eitheralone or as a component of a kit, or may be prepared by the end user. Byway of non-limiting example, antibodies used in accordance with thepresently described embodiments may include one or more primaryantibodies, one or more secondary antibodies, or one or more primaryantibodies in combination with one or more secondary antibodies.

Suitable primary antibodies may include any antibodies selected by auser for use with the presently described system. In some embodiments,the primary antibody may be directed against a user defined antigen. Insome embodiments, the primary antibody may be a complex mixture ofantibodies recognizing a plurality of antigens. A primary antibody maybe purchased commercially or may be made by the user.

A primary antibody may be a polyclonal antibody or a monoclonalantibody. A monoclonal antibody may be raised in mouse or in rat. Amonoclonal antibody may be IgG (IgG1, IgG2a, IgG2b, IgG3), IgM, IgA, IgDand IgE subclasses. A polyclonal antibody may be raised in rabbit,mouse, rat, hamster, sheep, goat, horse, donkey or chicken. In anembodiment, an antibody may be derived from human serum. A humanantibody may be at least partially or fully purified. Methods ofpreparing and purifying antibodies are widely known in the art. Generalguidance in the production, purification and use of various antibodypreparations may be found, for example, in the reference texts Harlow etal., 1989, Antibodies: A Laboratory Manual, Cold Spring Harbor, N.Y.,Harlow et al., 1999, Using Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory Press, N Y, and Harlow, et al., 1988, In: Antibodies,A Laboratory Manual, Cold Spring Harbor, N.Y., all of which are herebyexpressly incorporated by reference in their entirety.

In some embodiments, a primary antibody may be a “loading controlantibody”. The loading control antibody may be provided by the user ormay be provided commercially as part of the presently described system.Exemplary though non-limiting loading control antibodies that may beused or supplied with the presently described systems and methods mayinclude antibodies directed against actin, tubulin, histone, vimentin,lamin, GAPDH, VDAC1, COXIV, hsp-70, hsp-90 or TBP.

The concentration of primary antibody in an immunoblotting buffer willof course vary, depending on the specific primary antibody being used,the context in which the antibody is being used, and various otherproperties inherent in the antibody. The determination of an appropriateprimary antibody concentration to use in any given experimental scenariois well within the skill level of a practitioner having ordinary skillin the art. Typically, the concentration of the primary antibody will be1:10 to 1:20,000, 1:100 to 1:15,000, 1:1,000 to 1:10,000 or 1:1,500 to1:5,000.

Suitable secondary antibodies for use in accordance with the presentlydescribed systems and methods include any antibody capable ofrecognizing and binding to a primary antibody. A secondary antibody mayoptionally be coupled to one or more detection means. It will be readilyapparent to the skilled artisan that what constitutes a suitablesecondary antibody will of course vary, depending on the identity of theone or more primary antibodies used in conjunction with the secondaryantibody. Generally, a secondary antibody will be selected to bind to atleast a portion of the primary antibody being used. Selection of anappropriate secondary antibody further depends on the methods that willbe used to detect the signal in later steps. If an end user is using achemiluminescent technique to detect an analyte, then a suitablesecondary antibody may be coupled to, e.g., a peroxidase enzyme. If aninvestigator is using colorimetric techniques to detect an analyte, thena suitable secondary antibody may be coupled to, e.g., an alkalinephosphatase enzyme. If an investigator is using fluorometric techniquesto detect an analyte, then a suitable secondary antibody may be coupledto a fluorophore (including but not limited to FITC, TRITC, Texas-Red,Alexa-Fluor reagents, quantum dots, semiconductor nanocrystals, etc.).Optionally, a secondary antibody may be coupled to one or more biotinmoieties and the detection molecule (e.g., peroxidase, phosphates,fluorophore etc.) may be coupled to avidin or streptavidin. Using such abiotin/avidin system may, in some cases, amplify weak signals.Typically, the concentration of the secondary antibody will be 1:10 to1:20,000, 1:100 to 1:15,000, 1:1,000 to 1:10,000 or 1:1,500 to 1:5,000.

A suitable secondary antibody for use with the presently describedsystems and methods may be raised, for example, in rabbit, mouse, rat,hamster, pig, sheep, goat, horse, donkey, turkey or chicken. Thesecondary antibody will typically be raised in a different species thanthe species in which the primary antibody was raised. The secondaryantibody will be generated such that it recognizes and binds to aportion of the primary antibody. The secondary antibody may be at leastpartially affinity purified. The secondary antibody may be directedagainst mouse IgG, mouse IgA, mouse IgM, rat IgG, rat IgA, rat IgM,rabbit IgG, rabbit IgA, rabbit IgM, hamster IgG, hamster IgA, hamsterIgM, goat IgG, goat IgA, goat IgM, horse IgG, horse IgA, horse IgM,sheep IgG, sheep IgA, sheep IgM, donkey IgG, donkey IgA, donkey IgM,chicken IgG, chicken IgA, chicken IgM, chicken IgY, human IgG, humanIgA, or human IgM. A secondary antibody may be coupled to one or moredetection molecules such as, by way of example, alkaline phosphatase,peroxidase, biotin, a fluorophore or quantum dots or semiconductornanocrystals.

A blocking buffer may include an appropriate blocking reagent dissolvedor dispersed in a diluent. A suitable blocking reagent may include, byway of non-limiting example, whole serum, fractionated serum, bovineserum albumin, casein, soy protein, non-fat milk, gelatin, fish serum,goat immunoglobulin, rabbit immunoglobulin, mouse immunoglobulin, ratimmunoglobulin, horse immunoglobulin, human immunoglobulin, pigimmunoglobulin, chicken immunoglobulin or synthetic blocking reagents,such as those that may be obtained commercially from, e.g., BioFXLaboratories, Kem-En-Tec Diagnostics or GeneWay Biotech. A variety ofcommercially available pre-prepared blocking reagents are available, allof which may be supplied with a kit as described herein. Suchcommercially available blocking reagents include, though are not limitedto, e.g., WesternBreeze, I-BLOCK, BlockIt, PerfectBlock, SyntheticBlocking Buffer (BioFX Labs), Gelantis BetterBlock, SeaBlock, StartingBlock and Protein-Free Blocking Buffer (Pierce). In embodiments wherethe blocking reagent is supplied dissolved or dispersed in the diluent,the amount of the blocking reagent present may be in the range of about0.1 wt. % to about 50 wt. %, about 1 wt. % to about 40 wt. %, about 2.5wt. % to about 25 wt. %, about 5 wt. % to about 15 wt. % or about 10 wt%. In an embodiment, the amount of a blocking reagent present in animmunoblotting buffer may be up to about 75 mg/ml, up to about 50 mg/ml,up to about 40 mg/ml, up to about 30 mg/ml, up to about 20 mg/ml, up toabout 15 mg/ml, up to about 10 mg/ml up to about 5 mg/ml, up to about2.5 mg/ml, up to about 1 mg/ml, up to about 0.5 mg/ml, up to about 0.25mg/ml or up to about 0.1 mg/ml. Suitable diluents that may be used as acarrier medium for blocking reagents include any aqueous buffers havingsubstantially physiologic pH and ionic strength. Exemplary thoughnon-limiting diluents may include any buffer containing phosphate ions,bicarbonate, TAPS, Bicine, Tris, Bis-Tris, Tricine, HEPES, TES, MOPS,PIPES, Cacodylate, MES, acetate, ADA, ACES, cholamine, BES,acetamidoglycine or glycinaide present therein. Exemplary bufferssuitable for use as diluents may include, though are not limited to,e.g., PBS, Hank's solution, TBS, TE, TEN, or the like. Optionally, adiluent may include a detergent. Suitable detergents may includenon-ionic, non-denaturing detergents such as, e.g., Triton X-100, TritonX-114, NP-40, Brij-35, Brij 58, Tween-20, Tween-80, octyl glucoside andoctylthio glucoside and detergents such as sulfabetaines, includingSB-12, SB-14 and SB-16. A diluent may contain from about 0.01 vol. % toabout 5 vol. %, from about 0.05 vol. % to about 2 vol. %, from about 0.1vol. % to about 1.5 vol. %, or from about 0.5 vol. % to about 1 vol. %of a detergent.

In some embodiments, a suitable wash buffer may be the same as thediluent in which the blocking reagents are dispersed, as describedabove. In some embodiments, the wash buffer may be the diluent lackingone or more components thereof. In some embodiments, the wash buffer maybe the diluent lacking a blocking reagent.

In some embodiments, a wash buffer or a diluent may be supplied at fullstrength (i.e., 1X strength) or may be supplied as a concentratedsolution that facilitates storage and shipping thereof. A concentratedwash buffer or diluent may be diluted by the user using, for exampledeionized water, sterile water or any other suitable diluent.Concentrated wash buffers/diluents may be supplied as up to about 50×,up to about 25×, up to about 20×, up to about 10×, up to about 5× or upto about 2× strength.

In some embodiments, a wash buffer/diluent may be supplied to a user inone or more plastic or glass bottles supplied with the kit. Each kit mayinclude between 1 to 10 bottles of a wash buffer, between 1-5 bottles ofa wash buffer, or between 1-2 bottles of a wash buffer. Each bottle ofdiluent may contained up to 5 L, up to 4 L, up to 3 L, up to 2 L, up to1 L, up to 500 ml, or up to 100 ml of a diluent.

By way of example, embodiments of the bioprocessing cartridge asdescribed with respect to FIGS. 16-18 may be used in conjunction with abioprocessing device described herein to perform the cell separation,lysing, clarification, binding, washing, elution, precipitation and/orcollection steps of nucleic acid processing, including processing forcollection of nucleic acids such as DNA or fragments thereof, includingplasmid DNA, genomic DNA, viral DNA and bacterial DNA or fragments ofany of the above. An example of one embodiment of how such a process maybe conducted is follows. It should be understood that the followingprocedure is provided by way of example only and that one or more of thesteps may be modified and/or deleted and that other types ofbioprocessing may be performed using the bioprocessing device andbioprocessing cartridge and other protocols and the same or differentbioprocessing cartridge configurations:

1) A bioprocessing device is prepared for processing by inserting afluid reservoir holder for each sample to be processed into theremovable fluid holder tray and slid into the bioprocessing device. Eachfluid reservoir holder includes, a sample container into which thesample is inserted, a waste container, an RNase reservoir, aresuspension buffer reservoir, a lysis buffer reservoir, aneutralization buffer reservoir, a wash solution reservoir, an elutionsolution reservoir, an isopropanol reservoir, an ethanol reservoir, acollection buffer reservoir, and a collection reservoir, each reservoircontaining an appropriate amount of the relevant solution (or is emptysuch as for the waste and collection containers). The fluid reservoirholder may be supplied with empty reservoirs or with pre-filledreservoirs, with only the sample needing to be added. In someembodiments, one or more of the reservoirs may be pre-filled, while oneor more of the reservoirs may be filled by the user. In someembodiments, the fluid reservoir holder is supplied with at least onereservoir pre-filled, while in other embodiments, the fluid reservoirholder is supplied with no reservoirs and/or the one or more reservoirsare supplied empty.

2) For each sample to be processed, a bioprocessing cartridge isinserted into a slot of the bioprocessing device and secured to thecartridge holder. The fluid manifold for each cartridge is attached tothe control fluid connectors of the cartridge by inflating the bladderassociated with the cartridge holder. The operator ensures that theaspiration/expiration tubes are placed within the appropriate containerson the fluid container holder when inserting the cartridge into theslots and the cartridge holder.

3) The bioprocessing device may confirm proper insertion of the tray andthe cartridges.

4) The operator selects a desired protocol which may be pre-programmedinto the device or may be user-defined on the automated control systemfor the cartridges and initiates it. All of the access valves areensured to be closed at this time by verifying their actuation state.

The remainder of this example procedure will be described with respectto a single cartridge with reference to the reference numbers in FIGS.18 A-B, and occurs automatically and hands-free once the protocol isselected:

6) The automated control system, using pressure and/or vacuum throughthe appropriate control fluid channels opens membrane access valve 1818associated with the sample, actuates pump 1810 and pumps the samplethrough process fluid valves 1846 and 1852 associated with the processfluid channel connecting to the inlet at the upper central portion ofthe cell separation bioprocessing chamber 1803 on the cartridge, througha filter membrane in chamber 1803, out of the chamber through the outletof chamber 1803 at the bottom central portion of the chamber on the backor control fluid layer of the cartridge, through pass-through 1872 andback to the process fluid layer of the cartridge and out through accessvalve 1820 and into the waste container on the fluid container holder,actuating the appropriate valves open and closed as necessary to allowfluid to flow through the correct process fluid channels and to preventfluid from flowing down the wrong process fluid channels at the wrongtimes. The cells in the sample are captured on the filter in chamber1802.

7) Media remaining in the chamber 1803 and in the process fluid channelsleading to the chamber 1803 and in the pump 1810 is removed by blowingair, such as a pulse of air or a continuous stream of air, atapproximately 30-40 psi from the control fluid layer, through checkvalve 1868 to the process fluid layer, through pump 1810, process fluidvalves 1846 and 1852, across the filter in bioprocessing chamber 1803,out of the chamber 1803 through the outlet of chamber 1803 at the bottomcentral portion of the chamber 1803 on the back or control fluid layerof the cartridge, through pass-through 1872 and back to the processfluid layer of the cartridge and out through access valve 1820 and intothe waste container on the fluid container holder.

8) Using pump 1810, RNase is pumped from the RNase reservoir throughaccess valve 1822 into pump 1810, and through access valve 1824 and intothe resuspension buffer reservoir.

9) The cells on the filter membrane in chamber 1803 are resuspendedusing pump 1810, by pumping the resuspension buffer (with RNase) throughaccess valve 1824, through pump 1810, through process valve 1840 andpass-through 1872 where it is moved to the control fluid layer, throughthe outlet (used as an inlet this time) at the bottom central portion ofthe chamber 1803 on the back or control fluid layer of the cartridge,into chamber 1803 and across the filter (in the reverse direction fromthe cell separation in steps 6-7) out of the chamber 1802 through theinlet (used as an outlet this time) at the upper central portion of thecell separation bioprocessing chamber 1803, through process valve 1852and access valve 1826 and into the lysis buffer reservoir.

10) Any remaining cells in the chamber 1803 and in the process fluidchannels leading from chamber 1803 to the lysis reservoir are removed byblowing air, such as a pulse of air or a continuous stream of air, atapproximately 30-40 psi from the control fluid layer, through checkvalve 1868 to the process fluid layer, through process valve 1840 andpass-through 1872 where it is moved to the control fluid layer, throughthe outlet (used as an inlet this time) at the bottom central portion ofthe chamber 1803 on the back or control fluid layer of the cartridge,into chamber 1803 and across the filter (in the reverse direction fromthe cell separation in steps 6-7) out of the chamber 1803 through theinlet (used as an outlet this time) at the upper central portion of thecell separation bioprocessing chamber 1803, through process valve 1852and access valve 1826 and into the lysis buffer reservoir.

11) The cell are lysed by gently mixing the solution in the lysis bufferreservoir back and forth between the lysis buffer reservoir and theresuspension reservoir by pumping it using pump 1810 from the lysisbuffer reservoir, through access valve 1826, through process valve 1846,through pump 1810, through access valve 1824 and into the resuspensionbuffer reservoir and back again. This back and forth may occur as oftenas necessary to lyse the cells and the solution may ultimately end up ineither of the reservoirs.

12) Assuming the lysed cells are in the resuspension buffer reservoir,neutralization buffer is pumped, using pump 1810 from the neutralizationbuffer reservoir, through access valve 1828, through process valve 1846,through pump 1810, through access valve 1824 and into the resuspensionbuffer reservoir. The solution may be mixed by pumping through thisroute back and forth and the may end up ultimately in either reservoirwhere the layers formed are allowed to separate.

13) Assuming the lysed and neutralized cells are in the resuspensionbuffer, the lysate may be clarified by pumping, using pump 1810, thelysate through access valve 1824, through pump 1810, through processvalve 1848, into bioprocessing chamber 1804 through the inlet at the topcentral portion of the chamber, through a clarification filter withinchamber 1804, where the cellular and other debris is removed, out ofchamber 1804 through the outlet at the bottom central portion of thechamber on the control fluid layer, through pass-through check valve1870 to the process fluid layer, across check valve 1866 (while beingprevented by the valve from passing through to the control fluid layer),through pass-through 1874 back to the control fluid layer, intobioprocessing chamber 1806 through a bottom central inlet, across aDNA-binding solid phase extraction filter, membrane, disk or cassette,out of bioprocessing chamber 1806 through an outlet at the top centralportion of chamber 1806 on the process fluid layer, through processvalve 1858 and access valve 1818 and into the sample container, whichwill now serve as a waster container.

14) The solid phase extraction filter, membrane, disk or cassette iswashed by pumping wash solution from the wash solution container usingpump 1812, through access valve 1830, through pump 1812, through processvalve 1850, across check valves 1870 and 1866 while being prevented frompassing through them, through pass-through 1874 to the control fluidlayer, into bioprocessing chamber 1806 through a bottom central inlet,across a DNA-binding solid phase extraction filter, membrane, disk orcassette, out of bioprocessing chamber 1806 through an outlet at the topcentral portion of chamber 1806 on the process fluid layer, throughprocess valve 1858 and access valve 1818 and into the sample (waste)container.

15) After the wash step, any remaining wash solution is removed frombioprocessing chamber 1806, by blowing air, such as a pulse of air or acontinuous stream of air, at approximately 30-40 PSI from the controlfluid layer, through check valve 1866, to the process fluid layer,through pass-through 1874 where it is moved to the control fluid layer,through the inlet at the bottom central portion of the chamber 1806across the filter, out of the chamber 1806 through the outlet at theupper central portion of the bioprocessing chamber 1806, through processvalve 1858, and through access valve 1818 and into the sample (waste)container.

16) The bound DNA is eluted from the solid phase extraction filter,membrane, disk or cassette by pumping, using pump 1812, elution solutionfrom the elution solution reservoir, through access valve 1832, throughpump 1812, through access valve 1850, across check valves 1870 and 1866while being prevented from passing through them, through pass-through1874 to the control fluid layer, into bioprocessing chamber 1806 througha bottom central inlet, across a DNA-binding solid phase extractionfilter, membrane, disk or cassette, out of bioprocessing chamber 1806through an outlet at the top central portion of chamber 1806 on theprocess fluid layer, through access valve 1860, through pump 1814,through access valve 1834 and into the isopropanol reservoir.

17) The solution in the isopropanol container is mixed by gently mixingthe solution in the isopropanol container back and forth between theisopropanol container and the elution solution container by pumping itusing pumps 1814 and 1812 from the isopropanol container, through accessvalve 1834, through pump 1814, through process valve 1854, through pump1812, through access valve 1832 and into the elution solution containerand back again. This back and forth may occur as often as necessary tomix the solutions and the solution should ultimately end up in theisopropanol container.

18) The DNA is captured on a precipitator in bioprocessing chamber 1808by pumping using pump 1814, the solution in the isopropanol containerthrough access valve 1834, through pump 1814, through access valve 1856and through an inlet in an upper portion of bioprocessing chamber 1808,into chamber 1808, across a precipitator filter with in chamber 1808,out an outlet in a bottom portion of chamber 1808 on the control fluidlayer, through pass-through 1873, through process valve 1863 and accessvalve 1818 and into the sample (waste) container.

19) The precipitator is washed with ethanol by pumping ethanol from theethanol container using pump 1814, through access valve 1836, throughpump 1814, through access valve 1856 and through an inlet in an upperportion of bioprocessing chamber 1808, into chamber 1808, across aprecipitator filter with in chamber 1808, out an outlet in a bottomportion of chamber 1808 on the control fluid layer, through pass-through1873, through process valve 1863 and access valve 1818 and into thesample (waste) container.

20) The precipitator is dried by blowing air, such as a pulse of air ora continuous stream of air, at approximately 30-40 PSI from the controlfluid layer, through check valve 1864 to the process fluid layer,through process valve 1862, through an inlet in an upper portion ofbioprocessing chamber 1808, into chamber 1808, across a precipitatorfilter with in chamber 1808, out an outlet in a bottom portion ofchamber 1808 on the control fluid layer, through pass-through 1873,through process valve 1863 and access valve 1818 and into the sample(waste) container.

21) The DNA on the precipitator is eluted into the collection containerby pumping the collection buffer from the collection buffer containerusing pump 1816, through access valve 1838, through pump 1816, throughacross check valve 1864 while being prevented from passing through it,through process valve 1862, through an inlet in an upper portion ofbioprocessing chamber 1808, into chamber 1808, across a precipitatorfilter with in chamber 1808, out an outlet in a bottom portion ofchamber 1808 on the control fluid layer, through pass-through 1873,through access valve 1838 and into the collection container.

It should be understood that this procedure is by way of example onlyand should not be considered to be limiting in any way. Many differentprocedure can be used with the cartridge of FIGS. 18A-B and thecartridge may be configured in different manners according to differentprotocols, including to have additional or fewer bioprocessing chambers,different spatial orientations of any of the bioprocessing chambers, theinlets and outlets to the bioprocessing chambers, different flow channelconfigurations, different numbers, types and spatial orientations ofpumps and valves, different numbers and types of containers and processsolutions, and different types of samples for processing.

Any suitable buffer, wash solutions, resuspension buffer, lysis buffer,neutralization buffer, RNase, elution/collection buffer, orprecipitation buffer may be used with or without any additional suitablereagents depending on the protocol being performed. Suitable buffers, aswell as there compositions and methods of use are disclosed in thefollowing U.S. patent references: U.S. Pat. No. 6,914,137, 2006/0154247,2007/0117972, U.S. Pat. Nos. 6,242,220, 5,990,301, 7,214,508, 7,109,322,and 6,297,371, all of which are hereby incorporated by reference asthough fully set forth herein.

Any suitable biologically acceptable buffer such as, e.g., Tris, TAPS,Bicine, Tricine, HEPES, TES, MOPS, PIPES, cacodylate, MES, acetate, orthe like, having pH between about 3.5 to about 9, between about 5 toabout 8, between about 6.5 to about 7.5 are suitable for use in thepreparation of a resuspension buffer in accordance with the presentlydescribed systems and methods. In some embodiments, a resuspensionbuffer may include between 1 mM to 100 mM, between 5 mM to 50 mM, orbetween 10 mM to 20 mM of a chelating agent such as, e.g., EDTA, EGTA,ALA, BAPTA, defarasirox, deferiprone, deferoxamine, DTPA, dimercaprol,DMPS, DMSA, or the like. In some embodiments, a resuspension buffer mayoptionally include RNase such as endoribonucleases and exoribonucleases,including RNase A, RNase H, RNase I, RNase III, RNase L, RNase P, RNasePhyM, RNase T1, RNase T2, RNase U2, RNase V1, RNase V, PNPase, RNase PH,RNase II, RNase R, RNase D, RNase T, Exoribonuclease I, ExoribonuicleaseII and the like. In some embodiments, the RNase A formulation mayinclude 2.4 mg/ml RNase A, 50 mM Tris-HCL with a pH of 8.0, and 10 mM ofEDTA. In some embodiments, a resuspension buffer may optionally includelysozyme. In some embodiments, a resuspension buffer may optionallyinclude between about 1 mM to about 500 mM, between about 10 mM to about200 mM, between about 20 mM to about 100 mM, between about 30 mM toabout 75 mM of a carbohydrate such as a sugar. Exemplary sugars includeglucose, fructose, galactose, mannose, maltose, lactose, and the like.An exemplary resuspension buffer may include an aqueous solutioncontaining 50 mM Tris, pH 7.4, 100 μg/ml RNase A1, 10 mM EDTA, and 5 mMglucose. In some embodiments the resuspension buffer may include anaqueous solution including 50 mM Tris with a pH of 8.0, and 10 mM EDTA.

Suitable lysis solutions or buffers may include, in an aqueous carriermedium, one or more denaturants in combination with one or more lipiddisruptive agents. The denaturants may be nucleic acid denaturants such,e.g., an alkaline salt. Suitable alkaline salts may include sodiumhydroxide, potassium hydroxide, calcium hydroxide, and the like.Suitable lipid disruptive agents may include ionic surfactants.Exemplary ionic surfactants include sodium cholate, Sodiumdodecylsulfate (SDS), sodium deoxycholate (DOC), N-lauroylsarcosinesalts, cetyltrimethylammoniumbromide (CTAB),Bis(2-ethylhexyl)sulfosuccinate salts, and the like. In someembodiments, the lysis buffer ay be a formulation including 1% SDS and200 mM Sodium Hydroxide.

An exemplary lysis solution may include an aqueous solution containingbetween about 10 mM to about 500 mM, from about 50 mM to about 250 mM orfrom about 100 mM to about 200 mM NaOH, in combination with up to about10% SDS, up to about 5% SDS or up to about 1% SDS. Additional agents maybe present in the lysis buffer, as will be readily apparent to oneskilled in the art.

Suitable neutralization solutions may include, in an appropriate aqueouscarrier medium, one or more agents capable of neutralizing thesurfactants/alkaline solution present in the lysis solution. In someembodiments, a neutralization solution may include between about 0.5 Mto about 5 M of an appropriate acetate salt, having pH>4. An exemplaryneutralization solution may include an aqueous solution of about 3 Mpotassium acetate, pH˜5.

A suitable wash buffer may include, in an appropriate aqueous carriermedium, between 0.1 mM to about 100 mM salt, between about 0.5 mM toabout 500 mM of an appropriate biological buffer such that the pH of thewash buffer is at least about 6.0 or higher, and at least 5 vol. %, atleast 10 vol. % or at least 15 vol. % of an appropriate alcohol such asethanol or isopropyl alcohol. Optionally, a wash buffer may includebetween about 0.01 vol. % to up to about 10 vol. % of a suitablenon-ionic detergent such as, e.g., TRITON® X-100, CHAPS or NP-40. Theaddition of such a detergent may, in some embodiments, enhance theremoval of unwanted endotoxins from the preparation. An exemplary washbuffer may include 1 M NaCl, 50 mM MOPS, pH>8.0, 15 vol. % isopropylalcohol and 0.5 vol. % TRITON® X-100. In some embodiments, the washbuffer may include an aqueous solution including 800 mM NaCl and 100 mMsodium acetate Trihydrate with a pH of 5.0. In some embodiments, thewash buffer may be a formulation including, e.g., 1.5 NaCl, 100 mmSodium Acetate Trihydrate at a pH of 5.0.

A suitable collection/elution buffer may include, in an appropriateaqueous carrier medium, up to about 50 mM of an appropriate biologicalbuffer having 5.0<pH<9.0 and up to about 10 mM of an appropriatechelating agent. An exemplary collection/elution buffer may include 10mM Tris HCL with a pH of 8.0 in combination with 1 mM EDTA.

In some embodiments, an equilibration buffer may optionally be passedthrough the solid support matrix prior to the use thereof. Anequilibration buffer may include up to 1 M of a salt, up to 500 mM of anappropriate biological buffer having 5.0<pH<9.0, up to about 10 vol. %of an appropriate non-ionic detergent and up to about 20 vol. % alcohol.An exemplary equilibration buffer may include, e.g., 750 mM NaCl, 50 mMMOPS, pH 7, 15 vol. % isopropyl alcohol, and about 0.15 vol % TRITON®X-100.

In some embodiments, a precipitation buffer may optionally be passedthrough the solid support matrix prior to the use thereof. Aprecipitation buffer may include up to 5 M potassium acetate, up to 500mM of an appropriate biological buffer having 5.0<pH<9.0. An exemplaryprecipitation buffer may include, e.g., 3.1 M Potassium Acetate with apH of 5.5.

Further provided herein is an alternate method of purifying nucleic acidusing an embodiment of a bioprocessing device including one or more of:selecting the number of cartridges to be used; inserting the cartridgesinto a bioprocessing device; inflating the bladder to further stabilizethe cartridge; pumping cells from the sample container through abioprocessing chamber into the waste container for 2100 secs with a pumpdelay of 700 ms between pumps to capture cells; releasing pressurewithin the cartridge for 1 second; aspirating Rnase into the cartridgefor 4 seconds using a pump with a delay of 800 ms between pump strokes;mixing the resuspension buffer with the lysis buffer by pumping theresuspension buffer into the lysis buffer reservoir for 50 secs using apump delay of 800 ms between pump strokes; pumping the resuspensionbuffer/lysis buffer mixture back to the resuspension buffer reservoirfor 80 using a pump with an 800 ms delay between pump strokes; pump theresuspension/lysis buffer mixture through the bioprocessing chamber withthe captured cells for 150 seconds using a pump with delay of 800 msbetween pump strokes to resuspend the cells; preset the valves for 1sec; mix the lysis/resuspension buffer solution with the cells for 100seconds using a pump delay of 1200 ms between pump strokes; pump theneutralization mixture into the reservoir containing the resuspendedcells and lysis/resuspension buffer solution for 60 seconds using a pumpdelay of 1200 ms between pump strokes; mix the neutralization mixturewith the resuspension/lysis buffer mixture for 270 seconds using a pumpdelay of 2500 ms between pump strokes; purge the Genomed waste from thesystem for 1 second; open one of the control fluid connectors for 3seconds; pumping the lysis/resuspension/neutralization buffer with cellsfor 400 seconds using a pump dealy of 2500 ms through a secondbioprocessing chamber to clarify DNA from the cellular debris and bindthe DNA in another bioprocessing chamber; the Genomed filter is thenwashed for 10 seconds using a pump delay of 800 ms; the valves are thenpreset for 1 second and the Genomed filter is allowed to air dry for 2seconds; an elution buffer is than pumped for 20 seconds through themembrane using a pump delay of 1100 ms and the eluted solution is thenmixed with isopropyl alcohol twice for 20 seconds using a pump delay of800 ms; the lines are then purged to waste for 1 second; a process valvethen opened in three seconds; the pressure in the cartridge is thenreleased for 1 second; the precipitated DNA mixture is the pumpedthrough another bioprocessing chamber with a PPTR membrane for 60seconds using a pump delay of 1100 ms to capture the DNA; 70% ETOH isthen pumped through the bioprocessing chamber for 20 second using a pumpdelay of 1100 ms; the remaining ETOH is then purged to waste for 1second; the PPTR membrane is then dried for 90 seconds; the pressure isthen released from the bioprocessing cartridge for 1 second; a finalelution solution is then pumped through the PPTR membrane for 120seconds using a pump delay of 3000 into a collection tube; once the runis complete, the bladder is then deflated for 20 second, so thecartridge can be removed. The entire protocol takes about 3690 secondsto run.

Additional embodiments, instruments, methods and cartridges aredescribed below. In the dimensions provided for the cartridge below,height is the Y axis going up and down, width is the X axis going leftto right and depth is the Z axis (or smallest dimension) going into thepage of an embodiment of the bioprocessing cartridge when viewed asshown in FIG. 13A.

IV. EXAMPLES

Unless otherwise stated in the Examples, the automated processing of thewestern blots was conducted using the upper process channel and valve onthe bioprocessing card. This channel is generally the channel associatedwith process valve 1227 in FIG. 12.

A. Examples 1 & 2

A western blot was performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C&1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIG. 24A) of which were compared to a manual method (FIG. 24B) asfollows:

Reagents and Equipment

NuPAGE® LDS Sample Buffer (Invitrogen cat# NP0007)

NuPAGE® MES SDS Running Buffer (Invitrogen cat# NP0002)

NuPAGE® Reducing Agent (Invitrogen cat# NP0004)

SeeBlue® Plus2 Prestained Standard (Invitrogen cat# LC5925)

NuPAGE® Antioxidant (Invitrogen cat# NP0005)

Gels=NuPAGE® 4-12% BT IPG Well (Invitrogen cat# NP0330BOX)

iBlot Gel Transfer Device (Invitrogen cat# IB1001)

iBlot Regular Transfer Stack—Mini (nitrocellulose) (Invitrogen cat#IB3010-02)

WesternBreeze® Chromogenic Kit—Anti Rabbit (Invitrogen cat# WB7105)

Rabbit anti-E. coli antibody (Dako cat# B0357)

Protocol

1. Western Blot Preparation:

4 μg of an E. coli lysate were prepared in NuPAGE LDS sample buffer and5 μl SeeBlue® Plus2 standard and were loaded onto a NuPAGE 4-12% BT IPGwell format gel and run at 200V for 34 minutes. The proteins on the gelwere then transferred onto a nitrocellulose membrane (iBlot RegularTransfer Stack) using an iBlot Gel Transfer Device according to theinstructions in the users manual provided with the device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® Chromogenic Kit as described inthe user's manual provided with the kit. The Dako anti-E. coli primaryantibody was diluted 1:1000 in primary antibody diluent. The secondaryantibody used was the ready to use alkaline phosphatase conjugated goatanti-rabbit antibody contained in the WesternBreeze® Chromogenic Kit.Sufficient reagents were prepared in one batch to process both the blotprocessed with the automated instrument and the blot processed using themanual method (see below).

3. Blot Processing:

The nitrocellulose membrane (after transfer) described in section 1 ofthis protocol was cut in half, one half used for an immunodetectionperformed in the automated instrument, the other half processed usingthe standard manual procedure as described in the WesternBreeze®Chromogenic Kit user manual in a Falcon dish provided with the kit.

4. Automated Instrument:

The following reagents were loaded into an embodiment of the tray of theautomated instrument as shown in FIG. 6: blocker, rinse (water), Primaryantibody, Wash (WesternBreeze® wash buffer), Secondary Antibody, Wash(WesternBreeze® wash buffer—a second aliquot), rinse (water—a secondaliquot). A bioprocessing cartridge was inserted into a slot of theinstrument, half of the blot membrane was loaded into an embodiment of ablot holder as shown FIG. 21A (made from die cut PVC film) and insertedinto the bioprocessing chamber of the bioprocessing cartridge in theinstrument.

5. Automated Protocol:

After insertion of the blot into the bioprocessing cartridge a protocolwas initiated on the instrument, the protocol consisting of thefollowing steps, each iteration/step being performed automatically withno further human interaction required, though the progress of each stepand of the protocol was indicated on the GUI.

a. Block: 1×30 minutes—WesternBreeze® blocker

b. Rinse: 2×5 minutes—Water

c. Primary Antibody: 1×60 minutes—1:1000 rabbit anti-E. coli antibody inantibody diluent

d. Wash: 4×5 minutes—WesternBreeze® wash buffer

e. Secondary Antibody: 1×30 minutes—WesternBreeze® goat anti-rabbit APconjugate

f. Wash: 4×5 minutes—WesternBreeze® wash buffer

g. Rinse: 3×2 minutes—Water

For each iteration of the above steps, the time indicated did notinclude the filling time of the chamber with the relevant reagent andonly represents the recirculation time of the reagent through thechamber. At the end of each iteration of each of the steps the chamberwas drained before starting the next iteration/step and the drain timeis also not included in the indicated time. The filling/drain times wererelatively short, on the order of about 1 minute for all of the steps oriterations. As used herein and throughout the Examples a number followedby an “X” followed by a time is intended to represent the number ofiterations of that step performed for the indicated time. Thus, asincluded above “Rinse: 2×5 minutes” means 2 iterations of filling of thechamber with water, recirculation of the water for 5 minutes anddraining of the water, or, in other words filling of the chamber withwater, recirculation of the water for 5 minutes and draining of thewater (1 iteration) followed by filling of the chamber with water,recirculation of the water for 5 minutes and draining of the water(2^(nd) iteration).

The manual method used the same lengths of times and number ofiterations for each step as the automated method, but eachiteration/step was performed by hand. A summary of the manual method isas follows: The half of the blot for manually processing was firstplaced in the Falcon dish supplied with the WesternBreeze® Chromogenickit, blocker was poured into the dish and the dish was placed on arotator table for 30 minutes. After 30 minutes, the blocker was pouredoff by hand and the rinse water was added by hand. This method ofmanually adding reagents, rotating/incubating for a set time, pouringoff, then adding the next reagent was repeated for each iteration ofeach step listed above for the automated instrument, except they wereperformed manually.

6. Visualization:

After the incubation steps above were completed, both blot halves wererinsed with water and incubated in chromogenic substrate (fromWesternBreeze® Chromogenic kit) for 20 minutes. The results are shown inFIGS. 24 A & B.

B. Examples 3 and 4

A western blot was performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C&1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIG. 25A) of which was compared to a manual method (FIG. 25B) asfollows:

Reagents and Equipment

NuPAGE® LDS Sample Buffer (Invitrogen cat# NP0007)

NuPAGE® MES SDS Running Buffer (Invitrogen cat# NP0002)

NuPAGE® Reducing Agent (Invitrogen cat# NP0004)

SeeBlue® Plus2 Prestained Standard (Invitrogen cat# LC5925)

NuPAGE® Antioxidant (Invitrogen cat# NP0005)

Gels=NuPAGE® 4-12% BT IPG Well (Invitrogen cat# NP0330BOX)

iBlot Gel Transfer Device (Invitrogen cat# IB1001)

iBlot Regular Transfer Stack—Mini (PVDF) (Invitrogen cat# IB4010-02)

BupH™ Phosphate Buffered Saline (Pierce cat#28372)

Surfact-AMPs® 20 (Pierce cat#28320)

Non-fat dry milk (Carnation)

Goat anti-rabbit IgG HRP conjugate (Jackson cat#111-035-003)

Rabbit anti-E. coli antibody (Dako cat# B0357)

ECL HRP Western Blotting Substrate (Pierce cat#32209)

Transparency film for copiers (3M PP2500)

Fuji Luminometer (Fuji LAS-1000)

Protocol

1. Western Blot Preparation:

4 μg of an E. coli lysate was prepared in NuPAGE® LDS sample buffer and5 μl SeeBlue® Plus2 standard and was loaded onto a NuPAGE® 4-12% BT IPGwell format gel and run at 200V for 34 minutes. The proteins on the gelwere then transferred onto a PVDF membrane (iBlot Regular TransferStack) using an iBlot Gel Transfer Device.

2. Immunodetection Reagents Preparation:

a. PBST=2 packets of BupH Tris Buffered Saline+10 ml Tween 20 (1 vial ofSurfact-Amps 20) were combined and diluted to 1 L with deionized water.

b. Blocker=1.25 g non-fat dry milk (NFDM) was dissolved/diluted to 25 mlwith PBST.

c. Wash buffer=PBST

d. Primary Antibody Solution=25 ml of PBST was combined with 25 μl Dakoanti-E. coli primary antibody

e. Secondary 2° Ab Solution=25 ml PBST was combined with 5 μl JacksonHRP conjugated goat anti-rabbit IgG antibody.

3. Blot Processing:

The PVDF membrane (after transfer) described in section lof thisprotocol was cut in half, one half was used for an immunodetectionperformed on the automated instrument, the other half was processedusing the standard manual procedure as described in a Falcon dish suchas that provided in the WesternBreeze immunodetection kit.

4. Automated Instrument:

The reagents were loaded into an embodiment of the instrument tray asshown in FIG. 6, a bioprocessing cartridge was inserted into theinstrument, the half of the PVDF membrane was loaded into an embodimentof a blot holder as shown in FIG. 21A and was inserted into thebioprocessing chamber of the bioprocessing cartridge in the instrument.

5. Automated Protocol:

The following steps were performed using the automated instrument andmanually substantially as described in more detail in Examples 1-2above:

a. Block: 1×30 minutes—5% NFDM in PBST

b. Rinse: 2×5 minutes—Water

c. Primary Antibody: 1×60 minutes—1:1000 rabbit anti-E. coli antibody inPBST

d. Wash: 4×5 minutes—PBST

e. Secondary Antibody: 1×30 minutes—1:5000 goat anti-rabbit HRPconjugate in PBST

f. Wash: 4×5 minutes—PBST

g. Rinse: 3×2 minutes—Water

6. Visualization:

After the incubation steps above were completed, both membrane halveswere rinsed with water and placed side by side on a piece of plasticcopier transparency film. ECL HRP substrate was pipetted onto bothhalves and left to incubate for 1 minute. Excess substrate was pouredoff and another sheet of transparency film was placed on top of themembranes, creating a sandwich that was easy to handle and keeps theblots moist during imaging. This blot sandwich was imaged with the FujiLAS-1000 Luminometer for 3 minutes. The results are shown in FIGS. 25A &25B.

C. Examples 5-9

Four western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIGS. 26B-26E) were compared to a manual method (FIG. 26A) as follows:

Reagents and Equipment

NuPAGE® LDS Sample Buffer (Invitrogen cat# NP0007)

NuPAGE® MES SDS Running Buffer (Invitrogen cat# NP0002)

NuPAGE® Reducing Agent (Invitrogen cat# NP0004)

SeeBlue® Plus2 Prestained Standard (Invitrogen cat# LC5925)

NuPAGE® Antioxidant (Invitrogen cat# NP0005)

Gels=NuPAGE® 4-12% BT IPG Well (Invitrogen cat# NP0330BOX)

iBlot Gel Transfer Device (Invitrogen cat# IB1001)

iBlot Regular Transfer Stack—Mini (nitrocellulose) (Invitrogen cat#IB3010-02)

WesternBreeze® Chromogenic Kit—Anti Rabbit (Invitrogen cat# WB7105)

Rabbit anti-E. coli antibody (Dako cat# B0357)

Protocol

1. Western Blot Preparation:

Five blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE® LDS sample buffer and 5 μl SeeBlue® Plus2 standardand were loaded onto NuPAGE® 4-12% BT IPG well format gels and run at200V for 34 minutes. The proteins on the gels were then individuallytransferred onto nitrocellulose membranes (iBlot Regular Transfer Stack)using an iBlot Gel Transfer Device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® kit as described in the usermanual provided with the kit. The Dako anti-E. coli primary antibody wasdiluted 1:1000 in primary antibody diluent. The secondary antibody usedwas the ready to use alkaline phosphatase conjugated goat anti-rabbitantibody contained in the WesternBreeze® kit. Sufficient reagents wereprepared in one batch to process five blots—four using the automatedinstrument and one blot using the manual method.

3. Automated Instrument:

Four sets of the following reagents were loaded into an embodiment ofthe tray of the automated instrument as shown in FIG. 6: blocker, rinse(water), Primary antibody, Wash (WesternBreeze® wash buffer), SecondaryAntibody, Wash (WesternBreeze® wash buffer—a second aliquot), rinse(water—a second aliquot). Four bioprocessing cartridges were insertedinto individual slots in the instrument. Four blots from step 1 abovewere individually loaded into separate blot holders according to theembodiment of the blot holder as shown FIG. 21A and were inserted intothe bioprocessing cartridges within the instrument. The WesternBreeze®incubation protocol that is pre-programmed into the instrument was usedfor processing of these blots. All four blots in the instrument wereprocessed by the instrument simultaneously using the pre-programmedWesternBreeze® Protocol.

4. Automated Protocol:

The following steps were performed using the automated instrument andmanually substantially as described in more detail in Examples 1-2above:

a. Block: 1×30 minutes—WesternBreeze® blocker

b. Rinse: 2×5 minutes—Water

c. Primary Antibody: 1×60 minutes—1:1000 rabbit anti-E. coli antibody inPrimary antibody diluent

d. Wash: 4×5 minutes—WesternBreeze® wash buffer

e. Secondary Antibody: 1×30 minutes—WesternBreeze® goat anti-rabbit APconjugate

f. Wash: 4×5 minutes—WesternBreeze® wash buffer

g. Rinse: 3×2 minutes—Water

5. Visualization:

After the incubation steps above were completed, all blots were rinsedwith water and incubated in chromogenic substrate (from WesternBreezekit) for 20 minutes and imaged in the Fuji Luminometer (3 minuteexposure). Results are shown in FIGS. 26A-26E.

D. Examples 10A-B and 11A-B

Western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C&1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIGS. 27A and 27C) of which were compared to a manual method (FIGS. 27Band 27D) as follows:

Reagents and Equipment

NuPAGE® LDS Sample Buffer (Invitrogen cat# NP0007)

NuPAGE® MES SDS Running Buffer (Invitrogen cat# NP0002)

NuPAGE® Reducing Agent (Invitrogen cat# NP0004)

SeeBlue® Plus2 Prestained Standard (Invitrogen cat# LC5925)

NuPAGE® Antioxidant (Invitrogen cat# NP0005)

Gels=NuPAGE® 4-12% BT IPG Well (Invitrogen cat# NP0330BOX)

iBlot Transfer Device (Invitrogen cat# IB1001)

iBlot Transfer Stack—Mini (nitrocellulose) (Invitrogen cat# IB3010-02)

Novex® ECL Chemiluminescent Substrate Reagent Kit—(Invitrogen cat#WP200005)

Rabbit anti-E. coli antibody (Dako cat# B0357)

Goat Anti-Rabbit IgG—HRP Conjugate (Jackson Labs cat#111-035-003)

Pierce ECL (Thermo 32109)

Protocol

1. Western Blot Preparation: 4 μg of an E. coli lysate were prepared inNuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standard and wereloaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and run at 200Vfor 34 minutes. The proteins were then transferred onto a 0.2 μmnitrocellulose membrane (FIGS. 27A and 27B) or a 0.2 μm PVDF (FIGS. 27Cand 27D) membranes from the iBlot Regular Transfer Stacks using an iBlotGel Transfer Device according to the instructions in the user's manualprovided with the device.

2. Immunodetection Reagent Preparation:

The following reagents were used:

a. Blocker=5% non-fat dry milk (NFDM) in phosphate buffered saline with0.1% Tween 20

(PBST).

b. Wash buffer=PBST

c. Primary Antibody Solution=1:1000 dilution of Dako anti-E. coliprimary antibody in PBST.

d. Secondary 2° Ab Solution=1:5000 dilution of Jackson HRP conjugatedgoat anti-rabbit IgG antibody in PBST.

3. Blot Processing:

The membranes (after transfer) described in section 1 above were cut inhalf, one half of each were used for immunodetection performed in theautomated instrument, the other half of each was processed using thesame reagents and the standard manual procedure as described in theWesternBreeze® Chromogenic Kit user manual in a Falcon dish providedwith the kit.

4. Automated Instrument:

The following reagents were loaded into an embodiment of the tray of theautomated instrument as shown in FIG. 6: blocker, rinse (water), Primaryantibody, Wash (wash buffer), Secondary Antibody, Wash (wash buffer—asecond aliquot), rinse (water—a second aliquot). The individual halvesof the membranes were run separately as follows: a bioprocessingcartridge was inserted into a slot of the instrument, the half of theblot membrane was loaded into an embodiment of a blot holder as shownFIG. 21B (made from die cut PVC film) and inserted into thebioprocessing chamber of the bioprocessing cartridge in the instrument.

5. Automated Protocol:

The following steps were performed using the automated instrument (FIGS.27A and 27C) and manually (FIGS. 27B and 27D) substantially as describedin more detail in Examples 1-2 above:

a. Block: 1×30 minutes

b. Rinse: 2×5 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 4×5 minutes

e. Secondary Antibody: 1×30 minutes

f. Wash: 4×5 minutes

g. Rinse: 3×2 minutes

6. Visualization:

Visualization was performed substantially as described in Examples 3-4above. The results are shown in FIGS. 27A-27D.

E. Examples 12A & 12B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C&1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14:

1. Western Blot Preparation:

Two blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standardand were loaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and runat 200V for 34 minutes. The proteins were then transferred onto 0.2 μmPVDF membranes from the iBlot Regular Transfer Stacks using an iBlot GelTransfer Device according to the instructions in the user's manualprovided with the device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® Chromogenic Kit as described inthe user's manual provided with the kit. The Dako anti-E. coli primaryantibody was diluted 1:1000 in primary antibody diluent. The secondaryantibody used was the ready to use alkaline phosphatase conjugated goatanti-rabbit antibody contained in the WesternBreeze® Chromogenic Kit.Sufficient reagents were prepared in one batch to process both blots.

3. Automated Instrument:

Two sets of the following reagents were loaded into an embodiment of thetray of the automated instrument as shown in FIG. 6: blocker, rinse(water), Primary antibody, Wash (WesternBreeze® wash buffer), SecondaryAntibody, Wash (WesternBreeze® wash buffer—a second aliquot), rinse(water—a second aliquot). The two blot membranes were inserted intoseparate blot holders according to the embodiment of the blot holder asshown in FIG. 22B and were inserted into the bioprocessing chambers ofthe bioprocessing cartridges in the instrument.

4. Both blots were processed using the automated instrumentsubstantially as described in more detail in Examples 1-2 using thefollowing protocol:

a. Block: 1×10 minutes—WesternBreeze® blocker

b. Primary Antibody: 1×30 minutes—1:1000 rabbit anti-E. coli antibody inantibody diluent

c. Wash: 2×1 minutes and 2×5 minutes—WesternBreeze® wash buffer

d. Secondary Antibody: 1×30 minutes—WesternBreeze® goat anti-rabbit APconjugate

e. Wash: 2×5 minutes—WesternBreeze® wash buffer

f. Rinse: 3×1 minutes—Water

5. Visualization:

After the incubation steps above were completed, both blots were rinsedwith water and incubated in chemiluminescent substrate and imaged in theFuji Luminometer (3 minute exposure). The results are shown in FIG.28A-D.

F. Examples 13A & B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14:

1. Western Blot Preparation:

Two blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standardand were loaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and runat 200V for 34 minutes. The proteins were then transferred onto a 0.45μm nitrocellulose membrane (Example 13A) or a 0.45 μm PVDF membrane(Example 13B) using the method described in the NuPAGE Bi-Tris GelInstruction Booklet using 10% methanol and 1:1000 dilution ofantioxidant.

2. Immunodetection Reagent Preparation:

The following reagents were used:

a. Blocker=5% non-fat dry milk (NFDM) in Tris buffered saline (ThermoScientific) with 0.1% Tween 20 (TBST).

b. Wash buffer=TBST

c. Primary Antibody Solution=1:1000 dilution of Dako anti-E. coliprimary antibody in TBST.

d. Secondary 2° Ab Solution=1:5000 dilution of Jackson HRP conjugatedgoat anti-rabbit IgG antibody in TB ST.

3. Automated Instrument:

Two sets of the reagents were loaded into an embodiment of the tray ofthe automated instrument as shown in FIG. 6. Two blot membranescartridges were inserted into separate blot holders according to theembodiment of the blot holder as shown in FIG. 22B and were insertedinto the bioprocessing chambers of the bioprocessing cartridges in theinstrument.

4. Automated Protocol:

Both blots were processed using the automated instrument substantiallyas described in more detail in Examples 1-2 above using the followingprotocol:

a. Block: 1×60 minutes

b. Wash: 2×1 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 2×1 minutes, 1×15 minutes and 2×5 minutes

e. Secondary Antibody: 1×60 minutes

f. Wash: 2×1 minutes, 1×15 minutes and 2×5 minutes

5. Visualization:

Visualization was performed substantially as described in Examples 3-4above. The results are shown in FIGS. 29A and 29B.

G. Examples 14A&B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14:

1. Western Blot Preparation:

Two blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standardand were loaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and runat 200V for 34 minutes. The proteins were then transferred onto 0.2 μmnitrocellulose (Example 14A) and 0.2 μm PVDF (Example 14B) membranesfrom the iBlot Regular Transfer Stacks using an iBlot Gel TransferDevice according to the instructions in the user's manual provided withthe device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® Chromogenic Kit as described inthe user's manual provided with the kit. The Dako anti-E. coli primaryantibody was diluted 1:1000 in primary antibody diluent. The secondaryantibody used was the ready to use alkaline phosphatase conjugated goatanti-rabbit antibody contained in the WesternBreeze® Chromogenic Kit.Sufficient reagents were prepared in one batch to process both blots.

3. Automated Instrument:

Two sets of the following reagents were loaded into an embodiment of thetray of the automated instrument as shown in FIG. 6: blocker, rinse(water), Primary antibody, Wash (WesternBreeze® wash buffer), SecondaryAntibody, Wash (WesternBreeze® wash buffer—a second aliquot), rinse(water—a second aliquot). The two blot membranes were inserted intoseparate blot holders according to the embodiment of the blot holder asshown in FIG. 22B and were inserted into the bioprocessing chambers ofthe bioprocessing cartridges in the instrument.

4. Automated Protocol:

Both blots were processed using the automated instrument substantiallyas described in more detail in Examples 1-2 above using the followingprotocol:

a. Block: 1×10 minutes—WesternBreeze® blocker

b. Primary Antibody: 1×30 minutes—1:1000 rabbit anti-E. coli antibody inantibody diluent

c. Wash: 2×1 minutes and 2×5 minutes—WesternBreeze® wash buffer

d. Secondary Antibody: 1×30 minutes—WesternBreeze® goat anti-rabbit APconjugate

e. Wash: 2×5 minutes—WesternBreeze® wash buffer

f. Rinse: 3×1 minutes—Water

5. Visualization:

After the incubation steps above were completed, both blots were rinsedwith water and incubated in chemiluminescent substrate for 5 minutes andimaged in the Fuji Luminometer (3 minute exposure). The results areshown in FIGS. 30A and 30B.

H. Examples 15A-B and 16A-B

Western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIGS. 31A and 31C) of which were compared to a manual method (FIGS. 31Band 31D) as follows:

1. Western Blot Preparation:

Two blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standardand were loaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and runat 200V for 34 minutes. The proteins were then transferred onto a 0.2 μmnitrocellulose membrane (FIGS. 31C & 31D) or a 0.2 μm PVDF (FIGS. 31A &31B) membrane from the iBlot Regular Transfer Stacks using an iBlot GelTransfer Device according to the instructions in the user's manualprovided with the device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® Chromogenic Kit as described inthe user's manual provided with the kit. The Dako anti-E. coli primaryantibody was diluted 1:1000 in primary antibody diluent. The secondaryantibody used was the ready to use alkaline phosphatase conjugated goatanti-rabbit antibody contained in the WesternBreeze® Chromogenic Kit.Sufficient reagents were prepared in one batch to process both the blotsprocessed with the automated instrument and the blots processed usingthe manual method (see below).

3. Blot Processing:

The membranes (after transfer) described in section 1 of this examplewere cut in half, one half of each used for an immunodetection performedin the automated instrument, the other half of each was processed usingthe standard manual procedure as described in the WesternBreeze®Chromogenic Kit user manual in a Falcon dish provided with the kit.

4. Automated Instrument:

For each automated processing, the following reagents were loaded intoan embodiment of the tray of the automated instrument as shown in FIG.6: blocker, rinse (water), Primary antibody, Wash (WesternBreeze® washbuffer), Secondary Antibody, Wash (WesternBreeze® wash buffer—a secondaliquot), rinse (water—a second aliquot). A bioprocessing cartridge wasinserted into a slot of the instrument, the half of the relevant blotmembrane was loaded into an embodiment of a blot holder as shown FIG.22B and inserted into the bioprocessing chamber of the bioprocessingcartridge in the instrument.

5. Automated Protocol:

The following steps were performed using the automated instrument (theresults of which are shown in FIGS. 31A and 31C) and manually (theresults of which are shown in FIGS. 31B and 31D). For the automatedprocessing, the reagents were recirculated in the bioprocessing chamberof the bioprocessing cartridge using the channel associated with theprocess valve 1440 in FIG. 14 using the following protocol:

a. Block: 1×30 minutes

b. Rinse: 2×5 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 4×5 minutes

e. Secondary Antibody: 1×30 minutes

f. Wash: 4×5 minutes

g. Rinse: 3×2 minutes

6. Visualization:

After the incubation steps above were completed, the blots were rinsedwith water and incubated in chemiluminescent substrate for 5 minutes andimaged in the Fuji Luminometer (3 minute exposure). The results areshown in FIGS. 31A-31D.

I. Examples 17A-B and 18A-B

Western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14 as follows:

1. Western Blot Preparation:

Two blots were prepared as follows: 4 μg of an E. coli lysate wereprepared in NuPAGE LDS sample buffer and 3 μl SeeBlue® Plus2 standardand were loaded onto a NuPAGE 4-12% BT ZOOM IPG well format gel and runat 200V for 34 minutes. The proteins were then transferred onto a 0.2 μmPVDF membrane from the iBlot Regular Transfer Stacks using an iBlot GelTransfer Device according to the instructions in the user's manualprovided with the device.

2. Blot Processing:

The membranes (after transfer) described in section 1 of this examplewere cut in half, one half of each blot was used for an immunodetectionperformed in the automated instrument, the results of which are shown inFIGS. 32A and 32C and manually, the results of which are shown in FIGS.32B and 32D, using the NFDM/TBST reagents (FIGS. 32C and 32D) describedin Examples 13A-B or the NFDM/PBST reagents (FIGS. 32A and 32B)described in Examples 10A-B and 11A-B.

3. Automated Instrument:

For each automated processing, the reagents were loaded into anembodiment of the tray of the automated instrument as shown in FIG. 6: abioprocessing cartridge was inserted into a slot of the instrument, thehalf of the relevant blot membrane was loaded into an embodiment of ablot holder as shown FIG. 22B and inserted into the bioprocessingchamber of the bioprocessing cartridge in the instrument.

4. Automated Protocol:

The following steps were performed using the automated instrument (theresults of which are shown in FIGS. 32C and 32D) and manually (theresults of which are shown in FIGS. 32A and 32B). For the automatedprocessing, the reagents were recirculated in the bioprocessing chamberof the bioprocessing cartridge using the channel associated with theprocess valve 1440 in FIG. 14 using the following protocol:

a. Block: 1×30 minutes

b. Rinse: 2×5 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 4×5 minutes

e. Secondary Antibody: 1×30 minutes

f. Wash: 4×5 minutes

g. Rinse: 3×2 minutes

5. Visualization:

Visualization was performed substantially as described in Examples 3-4.The results are shown in FIGS. 32A-32D.

For each of Examples J-M, the following Bovine Serum Albumin (BSA)samples were prepared (separately for each Example) and loaded ontoNuPage 4-12% BT 10 mini well mini gels for BSA blots and run at 200V forapproximately 34 minutes:

5 μl of Sharp Prestained Standard (Invitrogen Cat# LC5800)

8 μl of Magic Mark XP Western Protein Standard (Invitrogen Cat# LC5602)

50 ng of BSA (5 μl of 10 ng/μl BSA) (BSA—Sigma Cat# A-3059)

25 ng of BSA (5 μl of 5 ng/μl BSA)

10 ng of BSA (5 μl of 2 ng/μl BSA)

J. Examples 19A & 19B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIG. 33B) of which were compared to the results (FIG. 33A) of a manualmethod as follows:

1. Western Blot Preparation:

One set of BSA samples as described above were loaded and prepared asdescribed above. The proteins were then transferred onto a 0.2 μmnitrocellulose membrane from the iBlot Regular Transfer Stacks using aniBlot Gel Transfer Device according to the instructions in the user'smanual provided with the device.

2. Immunodetection Reagent Preparation:

Blocker, wash buffer and primary antibody diluent were prepared usingreagents contained in the WesternBreeze® Chromogenic Kit as described inthe user's manual provided with the kit. The Dako anti-E. coli primaryantibody was diluted 1:1000 in primary antibody diluent. The secondaryantibody used was the ready to use alkaline phosphatase conjugated goatanti-rabbit antibody contained in the WesternBreeze® Chromogenic Kit.Sufficient reagents were prepared in one batch to process both blots.

3. Blot Processing:

The membrane (after transfer) described in section 1 above was cut inhalf, one half of each was used for an immunodetection performed in theautomated instrument (as shown in FIG. 33B), the other half of wasprocessed using the standard manual procedure as described in theWesternBreeze® Chromogenic Kit user manual in a Falcon dish providedwith the kit (as shown in FIG. 33A).

4. Automated Instrument:

For the automated processing, the following reagents were loaded into anembodiment of the tray of the automated instrument as shown in FIG. 6:blocker, rinse (water), Primary antibody, Wash (WesternBreeze® washbuffer), Secondary Antibody, Wash (WesternBreeze® wash buffer—a secondaliquot), rinse (water—a second aliquot). A bioprocessing cartridge wasinserted into a slot of the instrument, the half of the blot membranewas loaded into an embodiment of a blot holder as shown FIG. 22B andinserted into the bioprocessing chamber of the bioprocessing cartridgein the instrument.

5. Automated Protocol:

The following steps were performed using the automated instrument (theresults of which are shown in FIG. 33B) using the following protocol:

a. Block: 1×30 minutes

b. Rinse: 2×5 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 4×5 minutes

e. Secondary Antibody: 1×30 minutes

f. Wash: 4×5 minutes

g. Rinse: 3×2 minutes

6. Visualization:

After the incubation steps above were completed, both blots were rinsedwith water and incubated in chemiluminescent substrate and imaged in theFuji Luminometer (3 minute exposure). The blots were then rinsed andthen incubated with chromogenic substrate for 20 minutes, rinsed,allowed to dry somewhat and then imaged using an Epson 4990 scanner. Theresults for the chromogenic imaging are shown in FIGS. 33A and 33B. TheLoads from left to right are—5 μl Sharp Prestained Marker, 8 μl of 1:10dilution of MagicMark, BSA (50 ng, 25 ng, 10 ng).

K. Examples 20A & 20B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14 (the resultsof which are shown in FIG. 34B) and manually (the results of which areshown in FIG. 34A) substantially the same as in Examples 19A-B with theexception that the proteins were transferred onto a 0.2 μm PVDFmembrane. The results for the chromogenic imaging are shown in FIGS. 34A& 34B. The Loads from left to right are—5 μl Sharp Prestained Marker, 8μl of 1:10 dilution of MagicMark, BSA (50 ng, 25 ng, 10 ng).

L. Examples 21A & 21B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIG. 35A) of which were compared to the results (FIG. 35B) obtainedusing a manual method:

1. Western Blot Preparation:

One set of BSA samples as described above were loaded and prepared asdescribed above. The proteins were then transferred onto a 0.2 μmnitrocellulose membrane from the iBlot Regular Transfer Stacks using aniBlot Gel Transfer Device according to the instructions in the user'smanual provided with the device.

2. Blot Processing:

The membrane (after transfer) described in section 1 of this exampleabove was cut in half, one half of the blot was used for animmunodetection performed in the automated instrument (used as shown inFIG. 35A) and manually (used as shown in FIG. 35B) using the NFDM/TBSTreagents described in Examples 13A-B.

3. Automated Instrument:

For the automated processing, the reagents were loaded into anembodiment of the tray of the automated instrument as shown in FIG. 6: Abioprocessing cartridge was inserted into a slot of the instrument, thehalf of the blot membrane was loaded into an embodiment of a blot holderas shown FIG. 22B and inserted into the bioprocessing chamber of thebioprocessing cartridge in the instrument.

4. Automated Protocol:

The following steps were performed using the automated instrument (theresults shown in FIG. 35B) and manually (the results shown in FIG. 35A):

a. Block: 1×60 minutes

b. Wash: 2×1 minutes

c. Primary Antibody: 1×60 minutes

d. Wash: 2×1 minutes, 1×15 minutes and 2×5 minutes

e. Secondary Antibody: 1×60 minutes

f. Wash: 2×1 minutes, 1×15 minutes and 2×5 minutes

5. Visualization:

After the incubation steps above were completed, both blots were rinsedwith water and incubated in HRP chemiluminescent substrate and imaged inthe Fuji Luminometer (3 minute exposure). The blots were then rinsed andthen incubated with TMB HRP chromogenic substrate for 20 minutes,rinsed, allowed to dry somewhat and then imaged using an Epson 4990scanner. The results for the chromogenic imaging are shown in FIG. 33.The Loads from left to right are—5 μl Sharp Prestained Marker, 8 μl of1:10 dilution of MagicMark, BSA (50 ng, 25 ng, 10 ng).

M. Examples 22A & 22B

Two western blots were performed using an embodiment of the automatedprocessing device as shown in FIGS. 1C & 1D and an embodiment of thebioprocessing cartridge as shown in FIGS. 12, 13A-B and 14, the results(FIG. 36A) of which were compared to the results (FIG. 36B) obtainedusing a manual method substantially the same as in Examples 19A-B withthe exception that for the automated processing the reagents wererecirculated in the bioprocessing chamber of the bioprocessing cartridgeusing the channel associated with the process valve 1440 in FIG. 14. Theresults for the chromogenic imaging are shown in FIG. 34. The Loads fromleft to right are—5 μl Sharp Prestained Marker, 8 μl of 1:10 dilution ofMagicMark, BSA (50 ng, 25 ng, 10 ng).

Unless explicitly noted in the example, for Examples N-W all of thefluids, solutions, reagents, mixtures, waste, or any other fluidproducts of the example, were pumped/moved using the cartridge bydrawing the fluid up into the cartridge using an aspiration/expirationtube, access valve, and pump located on the card. Additionally, duringsome steps of the examples, the fluid may be passed through amembrane/bioprocessing chamber located in the cartridge after beingdrawn up into the cartridge and before being expelled out of thecartridge.

N. Examples 23

Nucleic acid purification was performed using the automated processingdevice shown in FIGS. 1A & 1B, and the cartridge shown in FIGS. 16-18,the results of which are shown in FIG. 37. The amount of genomic DNAcollected using the described protocol varied depending on whether aflow diffuser was incorporated with the device. The amount of genomicDNA was decreased by using a flow diffuser during pumping of the lysedcell mixture from the lysis buffer reservoir to the resuspensionbuffer/RnaseA buffer mixture reservoir during the resuspension andlysing of cells. The amount of genomic DNA 3710 detected using a systemincorporating a flow diffuser was less than the amount of genomic DNA3720 detected using a system without a flow diffuser. However, theamount of plasmid DNA detected using both devices 3730, 3740 remained ofcomparable value.

1. Cell Capture:

250 mL of E. Coli containing media was aspirated into the bioprocessingcartridge from a sample reservoir located outside the bioprocessingcartridge and passed through a bioprocessing chamber containing a Bla065membrane. The cells were filtered from the media and the clarified mediapassed out of the cartridge into a waste reservoir. 20 PSI of airpressure was then applied to the inlet side of the Bla065 cell capturemembrane to move residual media from the membrane and out of thecartridge and into the waste reservoir.

2. Resuspension and Lysing of Cells:

RnaseA solution was aspirated into the cartridge from an outside reagentreservoir, pumped out of the cartridge into a reagent reservoircontaining a resuspension buffer, and the RnaseA and resuspension buffermixed together by the cartridge. The resuspension burffer/RnaseA mixturewas then aspirated into the cartridge through the membrane to removecells captured by the capture membrane. The cells were removed from thecapture membrane and passed out of the cartridge into a reagentreservoir containing a lysis buffer. Approximately ¾ amount of the lysedcell mixture was then pumped from the lysis buffer reservoir back to theresuspension/RnaseA buffer mixture reservoir. 32 PSI of air pressure wasthen applied through the outlet side of the cell capture membrane toremove the remaining captured cells to the lysis buffer reservoir. Theremaining captured cells were then pumped from the lysis bufferreservoir to the resuspension/RnaseA mixture reservoir.

3. Neutralization—

Neutralization buffer was then pumped from the neutralization bufferreservoir to the reservoir containing the lysed cells. The lysedcells/neutralization buffer solution was then pumped back into the lysisbuffer reservoir. The device then pauses for three minutes to allow celldebris layer and clear lysate phase layer to separate.

4. Clarification/Binding—

Cell debris was then clarified by pumping the cell debris layer from thereservoir into the cartridge and through an Extra-Thick (Xthick) glassfiber clarification membrane and Anion Exchange DNA binding membrane andout of the cartridge and into the waste reservoir. An anion exchangewash buffer was then pumped from the anion exchange wash bufferreservoir into the cartridge, through the membrane, and out to the wastereservoir. 32 PSI of air pressure was then applied through the anionexchange membrane to ensure all waste was collected from the membraneinto the waste container. An anion exchange elution buffer was thenpumped from the anion exchange elution buffer into the cartridge,through the membrane, and out of the bioprocessing cartridge and into areagent reservoir containing isopropyl alcohol, to precipitate the pDNA.The elution buffer/isopropyl alcohol buffer solution was then mixed bypumping the mixture back into the anion exchange elution bufferreservoir. The elution buffer/isopropyl alcohol buffer solution was thenmixed one more time by pumping the mixture back from the anion exchangeelution buffer reservoir back into the isopropyl alcohol reservoir. Theelution buffer/isopropyl alcohol mixture was then passed through a PPTRmembrane (Bla065) to capture the precipitated pDNA. The remainder of themixture was then passed out of the cartridge and into the wastereservoir. 70% ETOH was then pumped from the ETOH reagent reservoir intothe cartridge, through the PPTR membrane, and out to the wastereservoir. The membrane was then air dried by passing 32 PSI of airthrough the membrane for 1.5 minutes and any waste passed out ofmembrane collected by the waste reservoir. A final TE elution buffer wasthen pumped from the TE elution buffer reservoir through the PPTRmembrane, and out to a collection tube. The amount of genomic DNAdetected using a device with a diffuser is compared to a device notusing a diffuser as shown in FIG. 37.

O. Example 24

Nucleic acid can be purified and captured using a bioprocessing systemdescribed in FIGS. 1A & 1B and the protocol below. As opposed to Example23, Example 24 includes partial flow diffused pumping stems, andpremixed the lysis and resuspension buffers together prior to cellresuspension.

1. Cell Capture—

250 mL of E. Coli containing media was aspirated into the bioprocessingcartridge from a disposable cell liner reservoir located outside thebioprocessing cartridge and passed through a bioprocessing chambercontaining a Bla065 membrane. The cells were filtered from the media andthe clarified media passed out of the cartridge into a waste reservoir.

2. Resuspension and Lysing of Cells—

RnaseA solution was aspirated into the cartridge from a reagentreservoir, passed out of the cartridge and into a reagent reservoircontaining a resuspension buffer. Lysis buffer was then pumped from thelysis buffer reservoir into reservoir containing the resuspension bufferand the RnaseA. The lysis/resuspension/RnaseA mixture was then aspiratedinto the cartridge through the membrane to remove and lyse cells fromthe cell capture membrane before collected into an external reservoir.The remaining cells are then pumped from the external into a secondreservoir.

3. Neutralization—

Neutralization buffer was pumped from the neutralization bufferreservoir to a separate reservoir. The cells from the second reservoirdescribed above are then pumped into the reservoir containing theneutralization buffer. The automated system paused for three minutes toallow the cell debris phase and the clear lysate phase to separate.

4. Clarification/Binding—

The cell debris was then clarified by using a diffuser pump to pump theneutralized cell material from the reservoir through an Extra-Thickglass fiber clarification membrane and an Anion Exchange DNA bindingmembrane and out to the waste reservoir. An anion exchange wash bufferwas then pumped from the anion exchange wash buffer reservoir throughthe membrane and out to the waste reservoir. 32 PSI of air was thenapplied through the anion exchange membrane and out to the wastereservoir. An anion exchange elution buffer is then pumped from theanion exchange elution buffer reservoir through the membrane and out areservoir containing isopropyl alcohol, where the pDNA is precipitated.The elution buffer and the isopropyl alcohol was then mixed by thecartridge transferring the mixture from the isopropyl alcohol reservoirto a second reservoir and then back to the isopropyl alcohol reservoir.The elution buffer/isopropyl alcohol mixture containing the precipitatedpDNA was then pumped through the bioprocessing chamber containing a PPTRmembrane to capture the DNA. The remainder of the media is transferredto waste. 70% ETOH was then pumped from the ETOH reservoir through thePPTR membrane and out to the waste reservoir. The membrane was then airdried with 32 PSI of air for 1.5 and any material released from the PPTRmembrane collected in the waste reservoir. A final TE elution buffer wasthen pumped from the TE elution buffer reservoir through the PPTRmembrane and collected in a collection tube. The DNA collected is shownin FIG. 38. The amount of genomic DNA 3810 and plasmid DNA 3820 detectedare indicated.

P. Example 25

Nucleic acid can be purified and captured using a bioprocessing systemdescribed in FIGS. 1A & 1B, and the bioprocessing cartridge shown inFIGS. 16-18, where the automated system is configured with varying pumpspeed and step timing.

1. Cell Capture—

250 mL of E. Coli containing media was aspirated into the bioprocessingcartridge from a disposable cell liner reservoir located outside thebioprocessing cartridge and passed through a bioprocessing chambercontaining a Bla065 membrane. The cells were filtered from the media andthe clarified media passed out of the cartridge into a waste reservoir.The system operates with an 800 ms pump delay between each stroke of thepump for a 21 minute capture time.

2. Resuspend and Lyse Cells—

RnaseA solution is pumped from the RnaseA solution reservoir into theresuspension buffer reservoir using an 800 ms pump delay between eachpump stroke for 5 seconds. The resuspension buffer and RnaseA is thenpumped back into the RnaseA solution reservoir and then back to theresuspension buffer reservoir using an 800 ms pump delay between eachpump stroke for 2 seconds. The resuspension/RnaseA buffer is then pumpedthrough the cartridge into the lysis buffer reservoir using an 800 mspump delay between each pump stroke for 1 minute. TheRnaseA/resuspension/lysis buffer is then mixed by transporting thesolution through the card from the lysis buffer reservoir into theresuspension/RnaseA buffer reservoir at using an 800 ms pump delaybetween each pump stroke for 1 minute. The lysis/resuspension/RnaseAmixture is then pumped through the membrane where the cells captured onthe cell capture membrane are removed from the membrane and lysed andthen transported to the lysis/resuspension/RnaseA reagent reservoir. Thepumping is done using 800 ms pump delay between each pump stroke for 1minute and 45 seconds. The lysis mixture with lysed cells is thenpumpled from to the lysis buffer reagent reservoir using a 1100 ms pumpdelay between each pump stroke for 1 minute and 45 seconds.

3. Neutralization—

The lysed cells are then pumped from the lysis buffer reagent reservoirto the neutralization buffer reagent reservoir using an 1100 ms pumpdelay between each pump stroke for 1 minute and 45 seconds. The solutionis then pumped using a diffuser from the neutralization reservoir to thelysis mixture reservoir using a 2500 ms pump delay between each pumpstroke for 4 and a half minutes. The device is then paused for 4 minutesto allow cell debris and clear lysate phases to separate.

4. Clarification/Binding—

The cell debris was then clarified using a diffuser pump to pump thecell debris and clear lysate phases through an Extra-Thick glass fiberclarification membrane and then through an Anion Exchange DNA bindingmembrane and then to the waste reservoir using a 2500 ms delay betweeneach pump stroke for 5 minutes and 30 seconds. An Anion exchange washbuffer solution was then pumped from the Anion exchange wash bufferreservoir through the Anion exchange membrane and out to the wastereservoir using 1100 ms delay between each pump stroke for 30 seconds.32 PSI of air pressure was then applied through the anion exchangemembrane to pass debris from the membrane into the waste reservoir. 2seconds after the air pressure application was ceased, an anion exchangeelution buffer was then pumped through the membrane and out to theisopropyl alcohol reagent reservoir using a pump between each pumpstroke with 1100 ms delay for 30 seconds. The elution buffer and theisopropyl alcohol buffer was then mixed by transferring the mixture to asecond reservoir and then back to the isopropyl alcohol buffer reservoirusing a 1100 ms delay between each pump stroke for 45 seconds. The wastelines were then purged using 32 PSI of air pressure with any waste inthe waste lines passing out to the waste reservoir. Two seconds afterair pressure application was ceased, the valves were opened to releasepressure. The system was then paused for 1 minute to allow precipitationto occur. The elution buffer/isopropyl alcohol mixture containing theprecipitated pDNA was then passed through a PPTR membrane (bla065) tocapture the DNA and the remainder of the mixture was passed out to thewaste reservoir using a 1100 ms delay between each pump stroke for 1minute. 70% ETOH was then aspirated into the cartridge from the ETOHreservoir and passed through the PPTR membrane and then out to wasteusing a pump with 1100 ms delay between each pump stroke for 25 seconds.Residual ETOH was removed from the line by applying 32 PSI of airpressure to the membrane. The system was paused for 1 second. Themembrane was then air dried by applying 32 PSI of air pressure through acheck valve and out to waste for 1.5 minutes. A TE elution buffer wasthen applied through the PPTR to elute the pDNA into a collection tubeusing a 2000 ms delay between each pump stroke for 5 minutes. The amountof genomic DNA (gDNA) 3910, 3920 detected and the amount of plasmid DNA(pDNA) 3930, 3940 detected is shown in FIG. 39.

Q. Example 26

Nucleic acid can be purified and captured using a bioprocessing systemdescribed in FIGS. 1A & 1B and the bioprocessing cartridge shown inFIGS. 16-18, where the automated system is configured with varying pumpspeed and step timing. Nucleic acid purification using partial flowdiffused pumping steps wherein the application of air pressure,premixing of lysis with resuspension buffer have been removed. Theexample also used the reagent reservoir tray as shown in FIGS. 8B-8F.This version of the protocol finalized the removal of genomic DNA (gDNA)contamination.

1. Capture Cells—

125 mL of E. coli media was aspirated into the cartridge from thedisposable cell liner reservoir and passed through a Bla065 membrane ofone of the bioprocessing chambers of the cartridge to filter cells fromthe media. The clarified media was the pumped out of the cartridge intothe waste reservoir using 700 ms pump delay between pump strokes with 15minutes capture time. Pressure was then released and the system pausedfor 1 second.

2. Resuspension and Lysis of Cells—

RnaseA solution was pumped through the cartridge from the RnaseA reagentreservoir to the resuspension buffer reservoir using an 800 ms pumpdelay between pump strokes for 4 seconds. The resuspension buffer/RnaseAbuffer mixture was then pumped to the lysis buffer reservoir using an800 ms pump delay between pump strokes for 45 seconds. Thelysis/resuspension/RnaseA mixture was then aspirated into the cartridgeand passed through the cell capture membrane. The captured cells werethen removed from the membrane and lysed and the lysed cells pumped intothe resuspension/RnaseA buffer mixture reservoir using 800 ms pump delaybetween pump strokes for 1 minute and 20 seconds.

3. Neutralization—

the lysed cell mixture was the pumped using a diffuser to a secondreservoir and back to the original reservoir using a 2500 ms pump delaybetween pump strokes for 3 and a half minutes. The waste lines were thenpurged using a check valve to blow 32 PSI of air pressure in thecartridge for 2 seconds. The system was then paused for 30 seconds toallow cell debris and the clear lysate phases to separate.

4. Clarification/Binding—

The cell debris was clarified using a diffuser pump to pump the celldebris through an Extra-Thick glass fiber clarification membrane in onebioprocessing chamber and then pumped through an Anion Exchange DNAbinding membrane in another bioprocessing chamber and then finallypumped into a waste reservoir using a 2500 ms delay between pump strokesfor 8 and a half minutes. The remaining debris and buffer solution isthen pumped to the waste container using a 2500 ms delay between pumpstrokes for 30 seconds. Any remaining mixture in the lysis bufferreservoir is then pumped to the waste container using a 2500 ms delaybetween pump strokes for 30 seconds. An Anion exchange wash buffer ispumped from Anion exchange wash buffer reagent reservoir through theAnion exchange membrane to remove the unwanted material out to the wastereservoir using an 800 ms delay between pump strokes for 15 seconds. AnAnion exchange elution buffer was then pumped through the membrane toelute the captured DNA material out to an isopropyl alcohol reagentreservoir using an 1100 ms delay between pump strokes for 30 seconds.The elution buffer and isopropyl alcohol buffer are then mixed bytransferring the mixture to a second reagent reservoir and then back tothe isopropyl alcohol reagent reservoir using an 800 ms delay betweenpump strokes for 30 seconds. The waste lines were then purged using 32PSI of atmospheric pressure, purging the waste to the waste reservoirfor 1 second. The pressure was then released by opening several valvelocated along the waste lines. The system was then paused for 2 minutesto allow the pDNA in the mixture to precipitate. The elutionbuffer/isopropyl alcohol buffer mixture with precipitated DNA was thenpumped through the PPTR membrane (bla065) to capture the precipitatedDNA while the remainder of the mixture flows out to waste using an 1100ms delay between pump strokes for 1 minute. 70% ETOH was then pumpedfrom the ETOH reagent reservoir through the PPTR membrane and out towaste. Residual ETOH was then removed from the line and out to waste byapplying 32 PSI through the line for 1 second. The membrane was then airdried by applying 32 PSI of air through a check valve through themembrane and into a waste reservoir. A final TE elution buffer wasapplied through PPTR membrane to elute the precipitated DNA using a 3000ms delay for 1 minute and 20 seconds. The amount of plasmid DNA 4010detected is shown in FIG. 40.

R. Example 27

Protein expression can be identified using a bioprocessing system shownin FIGS. 1C & 1D and the bioprocessing cartridge shown in FIGS. 12-14.In some embodiments, a nitrocellulose membrane maybe used with thesystem, such as a Hybond nitrocellulose membrane, although any suitablemembrane may be used with the system.

1. Samples:

A 3T3-L1 primordial cell line was differentiated into adipocytes cells.Insulin was then added to some of the samples to stimulate pAKTexpression. Each sample contained 10 ug differentiated 3T3-L1 adipocytelysates.

2. Protocol:

The samples were blocked for 60 minutes in a blocker, for example,SeaBlock/TBS/0.5% Tween 20. Any suitable blocker may be used includingMILK, BSA, other serums, IVGs. The sample was then washed two times forone minute using a wash buffer, for example TBS/0.05% Tween 20. Anysuitable wash buffer may be used including PBS. Additionally, thepercentage of components in the wash buffer may be varied. The samplewas then co-incubated in either 1/1000 AKT (rabbit) and pAKT (mouse) orGlut-4 (rabbit) and GADPH (moue) primary antibodies for at least 900minutes, or overnight, in a SeaBlock/TBS/0.05% Tween 20 blocker. Thesample was then washed three times for 5 minutes in a TBS/0.05% Tween 20wash buffer. The samples were then co-incubated for 60 minutes in either1 nM GAR-QDaot 625 and GAM-Qdot 800 or in 1 ug/mL GAR-AlexaFluor 790(AF790) and GAM-AlexaFluor 680 (AF680) secondary conjugates in blockercontaining 0.01% SDS. Any suitable label may be used including quantumdots (Qdot) nanocrystals, including QDots 625, 605, 655, 565, 585, 705,800, and 525, and microspheres. In some embodiments, the primaryconjugates may be Goat anti-Mouse IgG (GAM), Goat anti-Rabbit IgG (GAR),or streptavidin. In some embodiments, the sample may be conjugated to aClick-iT® label/imaging kit. In some embodiments, the secondaryconjugate may be GAM, GAR, or streptavidin. The sample was then washedthree times for 5 minutes in TBS/0.05% Tween 20 wash buffer. The samplewas then rinsed in water two times for five minutes.

3. Results:

The results of using Q-Dot® nanocrystals with the device describedherein are shown in FIGS. 41A-41F, FIGS. 42A-42C, and FIGS. 43A-43F.FIGS. 41A-41F show the results obtained using the device described inFIGS. 1C & 1D. FIGS. 41A-41C illustrates the results obtained where thegel was done on the benchtop, whereas FIGS. 41D-41F show the resultsobtained using the device described herein. FIGS. 41A & 41D illustratetwo gels run identifying the presence of AKT (rabbit) labeled withGAR-Qdot 625, FIGS. 41B & 41E illustrate two gels run detecting thepresence of pAKT (mouse)+GAM-Qdot 800, and FIGS. 41C & 41F illustratethe merged results of gels shown in FIGS. 41A & 41B and FIGS. 41D & 41E,respectively. The arrows indicated the lanes in which both AKT and pAKTwere detected.

FIGS. 42A-42C show the results obtained using the device described inFIGS. 1C & 1D. FIG. 42A shows the presence of AKT (rabbit) wherein AKThas been labeled with GAR-AlexaFluor 790. FIG. 42B shows the presence ofpAKT (mouse) wherein the pAKT has been labeled with GAM-AF680. FIG. 42Cshows an image of the gels shown in FIGS. 42A & 42B. The arrowsindicated the lanes in which both AKT and pAKT were detected.

FIGS. 43A-43F shows the presence of different proteins in the adipocytesand, more particularly, the presence of the same amount of proteinacross the gel. The result of FIGS. 43A-43F can be used to compare howmuch sample was loaded in each well on the gel using either Qdots orAlexaFlour dyes. FIG. 43A shows the presence of Glut-4(rabbit) labeledwith GAR-Qdot 625. FIG. 43B shows the presence of GADPH (mouse) labeledwith GAM-Qdot 800. FIG. 43C shows the merged image of FIGS. 43A & 43B.FIG. 43D shows the presence of Glut-4(rabbit) labeled with GAR-AF 790.FIG. 43E shows the presence of GAPDH (mouse) labeled with GAM-AF680.FIG. 43F shows the merged image of FIGS. 43D & 43E.

S. Example 28

Food safety analysis may be performed using a bioprocessing systemdescribed in FIGS. 16-18. Contamination of food with pathogenicmicroorganisms is one of the major concerns in the food industry.Traditional culture methods for food safety pathogen detection are timeconsuming and may take greater than 24 hours to perform, from start tofinish. Current requirements in food safety testing specify a rapiddetection of a small number of bacteria, typically 1 cubic foot per 25grams of a food sample, in less than 8 hours. These requirements makerapid detection of slow-growing bacteria challenging because of the lownumber of bacteria that may be present in the culture after a short (upto 6 hours) pre-enrichment step. The detection and identification ofbacterial pathogens in food may be done with DNA analysis, however,extraction, purification, and recovery of a sufficient amount ofbacterial DNA from large sample volumes may be a critical factor inthese assays. Because of the relatively low number of pathogenicbacteria in a culture even after 8 hours of enrichment (typically 0.1-10cfu/mL) recovering sufficient amounts of bacterial DNA for successfuldownstream PCR is essential. Insufficient numbers of DNA targets in PCRreactions can lead to high Ct values or no positive signal. Conventionalconcentrating techniques include techniques, such as centrifugation oflarge sample volumes (1 ml or more), co-precipitate bacteria, foodsample particulates and other inhibitors typically present in theculture. Therefore, robust DNA-extraction protocols have to be usedbefore PCR or other molecular techniques can be used. However,centrifugation of large volumes of culture enriched with pathogenicbacteria is associated with risks of damaging containers and as aresult, severe contamination of equipment and work area. Using thedevice provided herein in FIGS. 1A & 1B and the bioprocessing cartridgeshown in FIGS. 16-18, DNA can be prepared and extracted from a largesample volume using an automated method and device.

1. Sample Preparation:

a food matrix culture (10-50 mL) is applied to the prefilter (P). Theprefilter retains large size particulates and allows bacteria to flowthrough the filter. The flow-through, containing mostly bacteria is thendirected to the second filter where the bacteria is then captured by thefilter and the flow through discarded to waste. The bacteria captured bythe second filter is then lysed on the second filter using a lysissolution, for example, PrepSeq lysis solution, and the lysate isdirected to the silica membrane. The DNA from the lysed bacteria iscaptured by the silica membrane and the flow through is discarded to thewaste reservoir. The silica membrane is then washed with PrepSeq washsolution to remove PCR inhibitors.

2. DNA Collection:

an elution buffer, for example PrepSeq elution buffer, is then pumpedthrough the silica membrane to elute the DNA from the silica membrane.The amount of DNA eluted from the membrane may be between 40 uL-115 uL.

3. Results:

using the bioprocessing device herein allows for the processing ofextra-large volumes (>10 mL) of complex food sample cultures in arelatively short amount of time. The automated sample processing stepsallow removing food particulates from the sample matrix and capturingbacterial DNA extractions using the silica membrane.

T. Example 29

Nucleic acid can be purified and captured using a bioprocessing systemdescribed in FIGS. 1A & 1B and the bioprocessing cartridge shown inFIGS. 16-18, where the automated system is configured with varying pumpspeed and step timing. Nucleic acid purification using partial flowdiffused pumping steps wherein the application of air pressure,premixing of lysis with resuspension buffer have been removed. Theexample also used the reagent reservoir tray as shown in FIGS. 8B-8F.This version of the protocol optimized the removal of genomic DNA (gDNA)contamination.

1. Cell Capture:

125 mL of E. Coli containing media was aspirated into the bioprocessingcartridge from a sample reservoir (disposable cell liner reservoir)located outside the bioprocessing cartridge and passed through abioprocessing chamber containing a Bla065 membrane to filter cells fromthe media. The clarified media separated from the cells was pumped outof the cartridge into a waste reservoir. The sample was pumped throughthe bioprocessing chamber using a 700 ms pump delay for 15 min capturetime. Pressure remaining in the cartridge was released for 1 second.

2. Cell Resuspension and Lysis:

RnaseA solution was aspirated into the cartridge from an outside reagentreservoir and then pumped out of the cartridge into a reagent reservoircontaining a resuspension buffer. The RnaseA solution was pumped using800 ms pump delay for 4 seconds. The resuspension/RnaseA buffer mixturewas then mixed together. The resuspension/RnaseA buffer mixture was thenpumped from the buffer reservoir to the lysis buffer reservoir. Themixture was pumped using an 800 ms pump delay for 45 seconds. The lysisbuffer/resuspension/RnaseA mixture was then pumped from the lysis bufferreservoir through the outlet side of the membrane to simultaneouslyremove and lyse cells from the cell capture membrane. Pumping themixture through the outlet side of the membrane eliminated the need touse an air to remove the remaining cells captured cells. The mixture waspumped using an 800 ms pump delay for 1 minute and 20 seconds. Thediffused lysis buffer/resuspension/RnaseA mixture was pumped from to theresuspension/RnaseA mixture reservoir using a 2500 ms pump delay for 3minutes and 30 seconds.

3. Neutralization:

The lysed cells were then pumped from a first reservoir to a secondreservoir using a 2500 ms pump delay between each pump stroke for 3minutes and 30 seconds. The mixture was then diffuse pumped from thesecond reservoir to a third reservoir using a 2500 ms pump delay betweeneach pump stroke for 6 minutes and 40 seconds. The mixture was thendiffuse pumped from the third reservoir back to the second reservoirusing a 2500 ms pump delay for 5 minutes. The remainder of the mixturein the third reservoir was then diffuse pumped from the third reservoirback to the second reservoir using a 2500 ms pump delay for 5 minutes.The waste lines were then purged for 2 seconds using a check valve toapply 32 PSI of air. The device was then paused for 5 minutes to allowthe cell debris and clear lysate phases to separate.

4. Clarification/Anion Exchange Binding:

The cell debris was then clarified using a diffuser pump to pump thecell debris and clear lysate phases through an Extra-Thick glass fiberclarification membrane and then through an Anion Exchange DNA bindingmembrane and then to the waste reservoir using a 2500 ms delay for 10minutes and 30 seconds. Remaining debris and buffer was removed using a2500 ms delay for 1 minute. An anion exchange wash buffer was thenpumped through the Anion exchange membrane and out to the wastereservoir using a 2500 ms delay for 40 seconds

5. Anion Exchange Elution and Precipitation:

Anion exchange elution buffer was pumped from the buffer reservoirthrough the anion exchange membrane and out to a reservoir containingIsopropyl alcohol using an 1100 ms delay pump delay for 1 minute and 30seconds. The elution buffer and isopropyl alcohol buffer mixture wasthen mixed by pumping the mixture from the isopropyl reservoir to theelution buffer reservoir using an 800 ms delay for 20 seconds and thenback to the isopropyl alcohol reservoir using an 800 ms pump delay for30 seconds. The waste lines were then purged to waste using 32 PSI ofair pressure for 1 second. Pressure was then released by opening valves.The system was then paused for 2 minutes to allow for precipitation tooccur

6. Capture of pDNA on Precipitator Membrane:

The elution buffer/IPA mixture containing precipitated pDNA was diffusepumped through PPTR membrane (bla065) to capture DNA. The filteredbuffers were pumped out to waste using a pump delay of 2500 ms for 4minutes. 70% ETOH was then diffuse pumped from the ETOH reservoirthrough the PPTR membrane and then out to waste using a pump with a 2500ms delay between pump strokes for 30 seconds. Residual ETOH was removedfrom the line by applying 32 PSI of air pressure for 1 second throughvalves and out to waste. The membrane was then air dried by applying 32PSI of air through the check valve and out to waste for 1.5 minutes.

7. Final Elution into Collection Tube:

A TE elution buffer was then applied through the PPTR membrane to elutethe pDNA into a collection tube using a 3000 ms delay between pumpstrokes for 5 minutes.

U. Example 30

Cell clumping and the effect of adding NaCl to alleviated cell clumpingwas tested using the protocol described in Example 29 above. Theprotocol was run using a bioprocessing system described in FIGS. 1A & 1Band the bioprocessing cartridge shown in FIGS. 16-18.

Using the protocol described in Example 29 above, 250 mM NaCl was addedto 125 mL of cells located in the reagent tray. Overnight cultures wereprepared by the addition of 50 uL of TOP10/DH10B-T1R glycerol stocksolution to 1 L of fresh LB media containing 100 ug/ml Ampicillin. 125mL of bacterial culture was poured into the reagent reservoir. NaCl (5M)was added to the reservoir prior to starting a run using the device toachieve the desired NaCl concentration.

The effect of treating cells using 0.2M NaCl solution versus 0.5 M NaClsolution prior to capture of DH10B-T1R cells was compared and theresults of the comparison are shown in FIG. 44A. As shown in FIG. 44A,there was a small increase in the plasmid yield when using 0.2M NaClsolution as compared to the control, while the 0.5M NaCl solutionappeared to have a detrimental effect on the plasmid yield.

The effect of treating cells using a 250 mM NaCl solution versus using a300 mM NaCl solution prior to capture of Top10 cells was compared andthe result of the comparison are shown in FIG. 44B. As shown in FIG.44B, both concentrations of NaCl increased the plasmid yields obtainedfrom the Top10 cells as compared to the control, with a 55% increase inthe plasmid yield captured when using the 250 mM NaCl concentration anda 40% increase in the plasmid yield captured when using the 300 mM NaClconcentration.

V. Example 31

Cell clumping and the effect of adding NaCl to alleviated cell clumpingwas tested using the protocol described in Example 29 above. Theprotocol was run using a bioprocessing system described in FIGS. 1C & 1Dand the bioprocessing cartridge shown in FIGS. 16-18.

NaCl pretreatment of cells: 6.5 mL of 5M NaCl was added to 125 mL ofbacterial culture located in the reagent tray. Plasmid yield from cellswith no salt pretreatment (control) was compared to plasmid yieldobtained from cells pretreated with 250 mM NaCl.

FIG. 45A shows the plasmid yields obtained from low optical density (OD)TOP10 cells (cells with an average density of 1.85), and high opticaldensity TOP10 cells (cells with an average density of 2.4-2.5) ascompared to the plasmid yields obtained from TOP10 controls (no salttreatment). As shown in FIG. 45A, the plasmid yield collected for allTOP10 cells increased with the treatment of 250 mM NaCl, as compared tothe controls. The volume of the final sample collected after the runremained unaffected by the salt pretreatment, as shown in FIG. 45B.

W. Example 32

Cell clumping and the effect of adding NaCl to alleviated cell clumpingwas tested using the protocol described in Example 29 above. Theprotocol was run using a bioprocessing system described in FIGS. 1C & 1Dand the bioprocessing cartridge shown in FIGS. 16-18.

NaCl pretreatment of cells: 6.5 mL of 5M NaCl was added to 125 mL ofbacterial culture located in the reagent tray. Plasmid yield from cellswith no salt pretreatment (control) was compared to plasmid yieldobtained from cells pretreated with 250 mM NaCl.

FIG. 46 shows the plasmid yields obtained from DH10B-T1R cellspretreated with 250 mM of NaCl as compared to cells with no saltpretreatment. As shown in FIG. 46, the plasmid yield obtained from theDH10B-T1R cells was increased for the 250 mM NaCl pretreated cellsversus the control cells.

The terms and expressions which have been employed herein are used asterms of description and not of limitation, and there is no intention inthe use of such terms and expressions of excluding any equivalents ofthe features shown and described or portions thereof, but it isrecognized that various modifications are possible within the scope ofthe invention claimed. Thus, it should be understood that although thepresent invention has been specifically disclosed in part by preferredembodiments, exemplary embodiments and optional features, modificationand variation of the concepts herein disclosed may be resorted to bythose skilled in the art, and such modifications and variations areconsidered to be within the scope of this invention as defined by theappended claims. The specific embodiments provided herein are examplesof useful embodiments of the present invention and it will be apparentto one skilled in the art that the present invention may be carried outusing a large number of variations of the devices, device components,and methods steps set forth in the present description.

All references cited in this application are hereby incorporated intheir entireties by reference to the extent that they are notinconsistent with the disclosure in this application. It will beapparent to one of ordinary skill in the art that methods, devices,device elements, materials, procedures and techniques other than thosespecifically described herein can be applied to the practice of theinvention as broadly disclosed herein without resort to undueexperimentation. All art-known functional equivalents of methods,devices, device elements, materials, procedures and techniquesspecifically described herein are intended to be encompassed by thisinvention.

When a group of materials, compositions, components or compounds isdisclosed herein, it is understood that all individual members of thosegroups and all subgroups thereof are disclosed separately. When aMarkush group or other grouping is used herein, all individual membersof the group and all combinations and subcombinations possible of thegroup are intended to be individually included in the disclosure. Everyformulation or combination of components described or exemplified hereincan be used to practice the invention, unless otherwise stated. Whenevera range is given in the specification, for example, a temperature range,a time range, or a composition range, all intermediate ranges andsubranges, as well as all individual values included in the ranges givenare intended to be included in the disclosure.

We claim:
 1. A bioprocessing cartridge comprising: a first bioprocessingchamber, wherein the first bioprocessing chamber includes a first solidsupport, and wherein the first solid support is configured to filterdebris from cell lysate; a second bioprocessing chamber, wherein thesecond bioprocessing chamber includes a second solid support, andwherein the second solid support is configured to reversibly bindnucleic acids; a plurality of fluid channels in fluid communication withthe first and second bioprocessing chambers; one or more reagentreservoirs, wherein the one or more reagent reservoirs are in fluidcommunication with one or more of the first and second bioprocessingchambers; and at least one cartridge alignment guide.
 2. Thebioprocessing cartridge of claim 1, wherein the first solid support is acell lysate clarification filter.
 3. The bioprocessing cartridge ofclaim 2, wherein the cell lysate clarification filter is a glass fibercell lysate clarification filter.
 4. The bioprocessing cartridge ofclaim 1, wherein the second solid support comprises a solid phaseextraction disk, cassette or filter.
 5. The bioprocessing cartridge ofclaim 4, wherein the filter comprises an anion exchange membrane or asilica membrane.
 6. The bioprocessing cartridge of claim 1, wherein thesecond solid support comprises a plurality of beads.
 7. Thebioprocessing cartridge of claim 1, further comprising: a thirdbioprocessing chamber, wherein the third bioprocessing chamber includesa third solid support, and wherein the third solid support is configuredto separate cells from cell culture media.
 8. The bioprocessingcartridge of claim 7, wherein the third solid support is a cellseparation filter.
 9. The bioprocessing cartridge of claim 7, furthercomprising: a fourth bioprocessing chamber, wherein the fourthbioprocessing chamber includes a fourth solid support, and wherein thefourth solid support is configured to capture nucleic acids eluted fromthe second solid support.
 10. The bioprocessing cartridge of claim 9,wherein the fourth solid support is a precipitation filter.
 11. Thebioprocessing cartridge of claim 1, further comprising: a wash bufferreservoir, wherein the wash buffer reservoir contains a wash bufferconfigured for removal of endotoxins.
 12. The bioprocessing cartridge ofclaim 11, wherein the wash buffer includes a non-ionic detergent.